Opened 8 years ago

Closed 7 years ago

#37644 closed defect (fixed)

ccpnmr: tcl/tk 8.6 breaks spectrum rendering

Reported by: howarth@… Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 2.1.2
Keywords: Cc: g5pw (Aljaž Srebrnič)
Port: ccpnmr

Description (last modified by ryandesign (Ryan Schmidt))

The migration to tcl/tk 8.6 breaks the ccpnmr so that it can no longer render NMR spectra without crashing.
Confirmed that reverting tcl/tk to 8.5.13 and rebuilding py27-tkinter against this version restores full functionality.
The rendering under tcl/tk 8.6 fails with...

>>> Spectrum successfully opened
finished opening spectrum Expt_1 ghnhb_3D
X Error of failed request:  BadDrawable (invalid Pixmap or Window parameter)
  Major opcode of failed request:  70 (X_PolyFillRectangle)
  Resource id in failed request:  0x601811
  Serial number of failed request:  47218
  Current serial number in output stream:  47221

IMHO, the migration to tcl/tk 8.6 was premature and should be reverted until tcl/tk 8.6.1 is released.
It is unclear if the defect lies in tcl/tk or _tkinter of py27-tkinter.

Attachments (3)

Portfile.diff (687 bytes) - added by howarth@… 8 years ago.
Portfile.diff to autoupdate in post-activate to obtain fix
ccpnmr_update.patch.bz2 (1.8 MB) - added by howarth@… 8 years ago.
bzip2 of diff between ccpnmr site-packages subdirectory pre and post-update
ccpnmr.diff (5.2 KB) - added by g5pw (Aljaž Srebrnič) 7 years ago.

Download all attachments as: .zip

Change History (21)

comment:1 Changed 8 years ago by ryandesign (Ryan Schmidt)

Description: modified (diff)
Summary: tcl/tk 8.6 breaks spectrum rendering in ccpnmrccpnmr: tcl/tk 8.6 breaks spectrum rendering

I'm guessing at this point we won't be reverting tcl and tk back to 8.5; we'd rather move forward. If you'd like to make a case for that idea though the macports-dev mailing list would be a good place.

comment:2 Changed 8 years ago by g5pw (Aljaž Srebrnič)

Hmm... I'm not really a Tcl guru, so I honestly don't have any idea :/

comment:3 Changed 8 years ago by g5pw (Aljaž Srebrnič)

Cc: g5pw@… added

Cc Me!

comment:4 Changed 8 years ago by howarth@…

This is fixed upstream however the fix is only available via the update feature in ccpnmr.
On fink, this isn't a problem because PostInstScript is available to execute

%p/bin/python%type_raw[python] -O %p/lib/python%type_raw[python]/site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/update/UpdateAuto.py

I don't see a clean why to do this in MacPorts short of hardcoding this command into the install analysis startup script so that it updates every time it is launched.

Last edited 8 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

Changed 8 years ago by howarth@…

Attachment: Portfile.diff added

Portfile.diff to autoupdate in post-activate to obtain fix

comment:5 Changed 8 years ago by howarth@…

Please commit the attached Portfile.diff. It solves the display breakage in ccpnmr 2.2.2 from the upgrade to tcl/tkl 8.6 by adding a post-activate phase which runs the AutoUpdate.py script. I assume this should still work for binary builds of the package as the post-activate phase should still be executed, correct? Also, we have to use a post-activate phase because the AutoUpdate feature in ccpnmr is only functional when the supporting files are present in the installed python site-packages subdirectory.

Last edited 8 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:6 Changed 8 years ago by ryandesign (Ryan Schmidt)

Running a program's auto-update feature is not great; in fact we usually want any software in MacPorts to be neutered so that any auto-update features are disabled. What version will running the auto-update update it to? I expect the answer is "the latest", which means the user gets an unknown version of the software and not necessarily the one the port advertises. Let's ask upstream to provide a patch to fix the issue, and then apply that to the port instead.

comment:7 Changed 8 years ago by howarth@…

Small fixes to the python scripts do not result in new releases of ccpnmr so the fix for tcl/tk will be unavailable to us otherwise.
The only other option would be install ccpnmr 2.2.2, make archive of site-packages/ccpnmr/ccpnmr2.2/python/, AutoUpdate
and then diff the two to create a patch.

comment:8 Changed 8 years ago by howarth@…

IMHO, we are far more likely to destablize this package by attempting to hand apply the current autoupdates
than just to live with utilizing that feature. Also I doubt we will see another release of the 2.2.x series (as current
development is focused on the 3.0 release).

comment:9 Changed 8 years ago by howarth@…

From a build on fink, we would have to provide patch for the following files vs stock 2.2.2 if we don't utilize the autoupdate feature

site-packages/ccpnmr/ccpnmr2.2/python/memops/gui/FileSelect.py, site-packages/ccpnmr/ccpnmr2.2/python/memops/format/compatibility/downgrade/v_2_1_0/General.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/AnalysisPopup.py, site-packages/ccpnmr/ccpnmr2.2/python/grenoble/meccano/MeccanoPopup.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/Register.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/CopyAssignments.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/Analysis.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/WindowBasic.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/frames/PeakTableFrame.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditSpectrum.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditExperiment.py, site-packages/ccpnmr/ccpnmr2.2/python/paris/aria/AriaExtendNmrFrame.py, site-packages/ccpnmr/ccpnmr2.2/python/memops/general/Io.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/macros/ArgumentServer.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/frames/WindowFrame.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/ViewStructure.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/wrappers/Psipred.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/Util.py, site-packages/ccpnmr/ccpnmr2.2/python/memops/editor/SaveProjectFrame.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/BrowseResonances.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditPeakLists.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/LinkSeqSpinSystems.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/NewWindow.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditProfiles.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/format/gui/FormatConverter.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/format/process/makeChemShiftsFromPeakLists.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/CalcHnHaCoupling.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/FollowShiftChanges.py, site-packages/ccpnmr/ccpnmr2.2/python/memops/gui/ScrolledMatrix.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/LinkPeakLists.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditExperimentSeries.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/OpenSpectrum.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/CalcRates.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/DataAnalysisBasic.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/PeakBasic.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/CalcDistConstraints.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/AssignmentBasic.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/ViewRamachandran.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/MoleculeBasic.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/SecStructureGraph.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/ExperimentBasic.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/EntryCompletionFrame.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/eci/IsotopeLabeling.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/clouds/NoeMatrix.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/clouds/NoeRelaxation.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/clouds/MidgePopup.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/format/converters/CyanaFormat.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/format/converters/DataFormat.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/format/general/Constants.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/format/general/Conversion.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/pseudoPdb/coordinatesIO.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/mol2/chemCompsIO.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/xeasy/peaksIO.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/dyana/generalIO.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/general/Util.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/AddContourFile.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/InitRootAssignments.py, site-packages/ccpnmr/ccpnmr2.2/python/memops/universal/Url.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditPeakFindParams.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/popups/EditStructures.py, site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/analysis/core/StructureBasic.py, site-packages/ccpnmr/ccpnmr2.2/python/memops/format/compatibility/upgrade/v_2_0_4/Minor.py, site-packages/ccpnmr/ccpnmr2.2/python/cambridge/dangle/homology.tab, 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site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+A11+msd_ccpnRef_2007-12-11-10-13-18_00003.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+C+msd_ccpnRef_2007-12-11-10-13-18_00004.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+C00+msd_ccpnRef_2007-12-11-10-13-18_00005.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+C11+msd_ccpnRef_2007-12-11-10-13-18_00006.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+G+msd_ccpnRef_2007-12-11-10-13-19_00001.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+G00+msd_ccpnRef_2007-12-11-10-13-19_00002.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+G11+msd_ccpnRef_2007-12-11-10-13-19_00003.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+U+msd_ccpnRef_2007-12-11-10-13-20_00001.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+U00+msd_ccpnRef_2007-12-11-10-13-20_00002.xml, site-packages/ccpnmr/ccpnmr2.2/data/ccp/molecule/ChemComp/RNA+U11+msd_ccpnRef_2007-12-11-10-13-20_00003.xml, site-packages/ccpnmr/ccpnmr2.2/python/gottingen/PalesFrame.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/cosmos/generalIO.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/cosmos/chemShiftsIO.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/cosmos/projectIO.py, site-packages/ccpnmr/ccpnmr2.2/python/memops/gui/Scrollbar.py, site-packages/ccpnmr/ccpnmr2.2/python/ccp/format/nmrStar/sequenceIO.py and site-packages/ccpnmr/ccpnmr2.2/python/ccpnmr/format/converters/NmrStarFormat.py

comment:10 Changed 8 years ago by howarth@…

Also note that we have been using the AutoUpdate feature in a postinst script with ccpnmr for years with fink with no complaints.

comment:11 Changed 8 years ago by g5pw (Aljaž Srebrnič)

But maybe the changes are trivial, just propagated to a lot of files. Could you attach the actual source diff?

comment:12 in reply to:  11 Changed 8 years ago by howarth@…

Replying to g5pw@…:

But maybe the changes are trivial, just propagated to a lot of files. Could you attach the actual source diff?

The problem is that the updates, which appear to be limited to python script changes), are installed directly over the installed files in site-packages.
These files don't directly map to their uninstalled positions in the source tree. So you would have to install the patch over the installed python files
or attempt to manually detangle their moved positions (or creation if they are new python files) in the original source tree. Should we just remove this
package from MacPorts for now?

comment:13 Changed 8 years ago by howarth@…

Also note that upstream seems to only release new versioned releases when the compiled c code changes and sticks with their update method when the changes are limited to the
python scripts. The active development is now focused on the new 3.0 release based on SpecView instead of analysis so I doubt we will see another release of the 2.2.x series.

comment:14 Changed 8 years ago by howarth@…

The patch diff between the ccpnmr site-package subdirectories (with *.py, *.py_old and *.xml_old excluded) is 23.8 MB uncompressed and 1.9 MB bzip2 compressed.
Do you seriously want this in the ports directories?

Changed 8 years ago by howarth@…

Attachment: ccpnmr_update.patch.bz2 added

bzip2 of diff between ccpnmr site-packages subdirectory pre and post-update

comment:15 Changed 8 years ago by g5pw (Aljaž Srebrnič)

Sorry for the late response, there was no need for the 23.8 MB diff. Sometimes you see the same small changes all over, and those could be easily incorporated using a reinplace. I'll try to contact upstream to see if they can do an intermediate release, tcl8.6 compatibility looks like a good reason to do one.

comment:16 Changed 8 years ago by howarth@…

I strongly doubt that they will want to bother updating the tarball just to accommodate our needs since it requires them to also rebuild all of their prebuilt binaries.
If you refuse to properly fix this package, perhaps we should just at least add a message to the post install that it is broken and that the user must manually execute
/opt/local/bin/updateAll to resolve the issue. Leaving packages broken like this for long periods of time is unacceptable.

Changed 7 years ago by g5pw (Aljaž Srebrnič)

Attachment: ccpnmr.diff added

comment:17 Changed 7 years ago by g5pw (Aljaž Srebrnič)

Port was updated, the attached diff (ccpnmr.diff) should solve this problem. I'll commit it if it's OK with the maintainer.

comment:18 Changed 7 years ago by g5pw (Aljaž Srebrnič)

Resolution: fixed
Status: newclosed

Maintainer timeout. Commited in r107713.

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