March 2013 - macports-tickets - lists.macosforge.org

[MacPorts] #35879: gnuplot: workaround for non-C99-compliant compiler (_Bool)
by MacPorts 18 Mar '13

18 Mar '13

#35879: gnuplot: workaround for non-C99-compliant compiler (_Bool) --------------------------------------------+------------------------------- Reporter: mojca.miklavec.lists@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: Keywords: | Port: gnuplot --------------------------------------------+------------------------------- Following a report on the mailing list (gnuplot doesn't compile on Mac OS X 10.6 with Xcode 4.2 which doesn't have C99-compliant compiler) here's a patch that should solve the problem for that platform (and I hope that it will be applied upstream). If anyone else was bitten by this, please report. {{{ In file included from ./plot.h:46, from wxterminal/wxt_gui.h:113, from wxterminal/wxt_gui.cpp:96: ./mouse.h:189: error: variable or field 'set_ruler' declared void ./mouse.h:189: error: '_Bool' was not declared in this scope ./mouse.h:189: error: expected primary-expression before 'int' ./mouse.h:189: error: expected primary-expression before 'int' ./mouse.h:197: error: '_Bool' has not been declared In file included from wxterminal/wxt_gui.h:113, from wxterminal/wxt_gui.cpp:96: ./plot.h:53: error: '_Bool' does not name a type ./plot.h:54: error: '_Bool' does not name a type ./plot.h:55: error: '_Bool' does not name a type }}} https://sourceforge.net/tracker/index.php?func=detail&aid=3562307&group_id=… Disclaimer: I'm not able to test this patch since I don't have access to old Xcode on 10.6. -- Ticket URL: <https://trac.macports.org/ticket/35879> MacPorts <http://www.macports.org/> Ports system for Mac OS

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[MacPorts] #29531: python_select: command not found
by MacPorts 17 Mar '13

17 Mar '13

#29531: python_select: command not found -----------------------------------------+---------------------------------- Reporter: hansimglueck@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 1.9.2 Keywords: | Port: -----------------------------------------+---------------------------------- Hi MacPorties, I'm wondering about a strange bug. I have installed scipy, matplotlib and other scientific stuff. My commands were: {{{ sudo port install py26-wxpython py26-numpy py26-matplotlib sudo port install py26-scipy py26-ipyhton }}} yea, right to this point everything works fine and after a few hours its done... I started ipython and everything works fine too. But in standard python i did not work ... i figured out that i use the apple python version: {{{ hans: hans$ python Python 2.6.1 (r261:67515, Aug 2 2010, 20:10:18) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin }}} so i started: {{{ hans: hans§ python2.6 Python 2.6.6 (r266:84292, May 15 2011, 15:57:09) [GCC 4.2.1 (Apple Inc. build 5666)] on darwin }}} and yea it works fine.... ok so i checked my python_select installation from macports: {{{ hans: hans§ port installed | grep python_select ipython_select @0.1.0 (active) python_select @0.3_1 (active) }}} but when i type: {{{ hans: hans$ sudo python_select python2.6 sudo: python_select: command not found }}} So port says python_select is fine but the command does not work? any hints? i already tried selfupdate, upgrade outdated and clean --all python_select.... greets hans -- Ticket URL: <https://trac.macports.org/ticket/29531> MacPorts <http://www.macports.org/> Ports system for Mac OS

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[MacPorts] #38413: new port: Intrinsic Noise Analyzer
by MacPorts 17 Mar '13

17 Mar '13

#38413: new port: Intrinsic Noise Analyzer --------------------------+-------------------------------- Reporter: hmatuschek@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: --------------------------+-------------------------------- This application analyzes fluctuations of bio-chemical reaction networks defined in SBML. We use MacPorts to build application bundels for our releases anyway and we would like to allow our users to receive updates via MacPorts. This software depends on libSBML (#26238). I would volunteer to maintain this the the libsbml port, to keep it up-to-date. -- Ticket URL: <https://trac.macports.org/ticket/38413> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #38395: couchdb-devel @1.4.0a-20130227 Erlang R16B breaks couchdb build
by MacPorts 17 Mar '13

17 Mar '13

#38395: couchdb-devel @1.4.0a-20130227 Erlang R16B breaks couchdb build --------------------+----------------------------------- Reporter: jeff@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: couchdb-devel couchdb --------------------+----------------------------------- Build fails with the following after upgrading erlang to R16B, reported in #37641. {{{ /opt/local/bin/erlc mochifmt_std.erl /opt/local/bin/erlc mochiglobal.erl mochifmt_std.erl:6: parameterized modules are no longer supported mochifmt_std.erl:11: variable 'THIS' is unbound mochifmt_std.erl:14: variable 'THIS' is unbound mochifmt_std.erl:23: variable 'THIS' is unbound make[3]: *** [mochifmt_std.beam] Error 1 make[3]: *** Waiting for unfinished jobs.... mochifmt_records.erl:12: parameterized modules are no longer supported mochifmt_records.erl:19: variable 'Recs' is unbound make[3]: *** [mochifmt_records.beam] Error 1 }}} CouchDB ticket: https://issues.apache.org/jira/browse/COUCHDB-1696 Not sure what to do about this yet. Suggestions welcome. This almost certainly affects couchdb as well. I'll add a note here when I've tested it and know for sure. -- Ticket URL: <https://trac.macports.org/ticket/38395> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #38149: Update Gwyddion to version 2.31
by MacPorts 17 Mar '13

17 Mar '13

#38149: Update Gwyddion to version 2.31 ------------------------+-------------------------------- Reporter: feranick@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: gwyddion | Port: gwyddion ------------------------+-------------------------------- Gwyddion has been updated upstream to version 2.31 (it's in version 2.30 in macports). This ticket request for an update of the version in macports. Changelog: Translations updated: Czech, French, Russian, Spanish. Libraries libgwyprocess: Bogus normalisation/possible crash in gwy_data_field_area_dh() in presence of mask on non-square area was fixed. distribution if the area contains no data due to masking. libgwyprocess: gwy_data_field_area_dh() returns a reasonable empty distribution if the area contains no data due to masking. libgwyprocess: Radial PSDF normalisation was corrected to be really sampling-independent and correspond to the formula in user guide. libgwyprocess: Double-free error if the initial Delaunay triangulation step fails was corrected. libgwyprocess: Swapped x and y coordinates of spectra in serialisation were fixed. libgwyprocess: Added brick (3D) data support backported from Gwyddion 3 development branch. libgwydgets: Crashes upon clicking colour selection buttons were fixed. libgwydgets: 3D view false colour axis shows overlay, not height units in the overlay mode. libgwyapp: Visibility of false colour bar and mask are included in 3D view settings saved by ‘Set Defaults’. libgwyprocess: gwy_data_field_distort() actually works for destination field of different size than source. Modules APE DAX (new): Imports APE Research DAX files. Nanomagnetics (new): Imports Nanomagnetics NMI files. VTK export (new): Exports fields as VTK structured grid files. Magellan (new): Imports FEI Magellan SEM images. Extend (new): Extends a field by adding borders using several methods. Brickshow (new): Added a simple module for loading, visualising and data extracting from 3D volume data (Bricks) GWYXYZF (new): Imports and export Gwyddion Simple XYZ files. Seiko: Files starting ‘NPXZ000AFM’ are recognised and imported. XQP phase files should be read with a correct value scale and units. Shimadzu: Files of different version than 2 are recognised and loaded. Omicron flat: Crash while reading files with up and down traces but no retrace was fixed. Createc: Conversion of raw data to physical values was corrected. Nanoeducator: Keep relative coordinates of datafields, Material description decoding from CP1251, Attempt to fix current scale in spectroscopy. Nanoscantech: Scan names of new standard (inside Attributes) supported, Units and scan names recoding from CP1251. Nanoscope: F-Z spectra are imported (experimental). Pixmap: Manual font size range is limited by zoom. Inset bar length is remembered and used the next time if possible. Raw XYZ: Tolerance for ‘regular grid’ (which is not triangulated) was increased to 5% of pixel size to help people with poorly rounded data. Edge: New Sobel and Prewitt classic edge detection functions. Drift correction: Correction can be applied to all compatible channels and channels can be directly replaced with corrected ones. Line layer: Thick line end markers are drawn correctly to image targets. NetCDF: GXSM file metadata support was improved, images are flipped when appropriate. Fit sphere: Units of resulting quantities are set correctly. Omicron: Abscissae of single point spectra were corrected to match SCALA. Graph fit: It is possible to plot the difference between data and fit to a new graph. Graph fit, FD fit and Critical dimension: Curve and controls were switched, controls should no longer jump around, interfering with selection. Merge: ‘None’ merge mode which does not do any correlation search was actually implemented. Critical warnings and wrong smooth merging for some image combinations were fixed. ‘Second’ really means the image selected in the dialog now. Other Compatibility with GLib older than 2.26, accidentaly broken in 2.30, was restored. Desktop files in correct locations are updated with --enable-home- installation configure option. Standalone gwy python module on Win32 no nonger tries to load non- existent Gwyddion libraries. -- Ticket URL: <https://trac.macports.org/ticket/38149> MacPorts <http://www.macports.org/> Ports system for Mac OS

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[MacPorts] #38412: rpm, rpm45, rpm50, rpm51, rpm52, rpm53, rpm54: building with +docs variant fails if doxygen is not active
by MacPorts 17 Mar '13

17 Mar '13

#38412: rpm, rpm45, rpm50, rpm51, rpm52, rpm53, rpm54: building with +docs variant fails if doxygen is not active -------------------------+------------------------------------------------- Reporter: | Owner: n3npq@… ryandesign@… | Status: new Type: defect | Milestone: Priority: Normal | Version: 2.1.3 Component: ports | Port: rpm, rpm45, rpm50, rpm51, rpm52, Keywords: haspatch | rpm53, rpm54 -------------------------+------------------------------------------------- {{{ $ sudo port deact doxygen ---> Deactivating doxygen @1.8.3.1_0+universal $ sudo port build rpm54 +docs -universal ---> Computing dependencies for rpm54 ---> Fetching distfiles for rpm54 ---> Verifying checksum(s) for rpm54 ---> Extracting rpm54 ---> Configuring rpm54 Error: org.macports.configure for port rpm54 returned: configure failure: command execution failed Please see the log file for port rpm54 for details: /opt/local/var/macports/logs/_Users_rschmidt_macports_dports_sysutils_rpm54/rpm54/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port rpm54 failed }}} Log contains: {{{ checking for doxygen... no configure: error: RPM API docs need doxygen in PATH }}} doxygen is typically a build dependency, not a runtime dependency. Also it should be a port:-style dependency, not a bin:-style one. We don't want possibly old and/or broken doxygens the user might have installed elsewhere to satisfy the dependency; we want to use the MacPorts one that we more or less know will work. -- Ticket URL: <https://trac.macports.org/ticket/38412> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #38408: Requesting maintainer listing for libsodium
by MacPorts 17 Mar '13

17 Mar '13

#38408: Requesting maintainer listing for libsodium ----------------------------+-------------------------------- Reporter: brian.andrew@… | Owner: macports-tickets@… Type: request | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: haspatch | Port: libsodium ----------------------------+-------------------------------- I'd like to be listed as the maintainer for libsodium. Attached is a patch reflecting this change. -- Ticket URL: <https://trac.macports.org/ticket/38408> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #38409: Update Portfile for The Silver Searcher to indicate openmaintainer
by MacPorts 17 Mar '13

17 Mar '13

#38409: Update Portfile for The Silver Searcher to indicate openmaintainer ---------------------------------+--------------------------------- Reporter: brian.andrew@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: haspatch maintainer | Port: the_silver_searcher ---------------------------------+--------------------------------- On the recommendation of cal and some additional reading, I'm submitting this patch to list openmaintainer for the_silver_searcher. -- Ticket URL: <https://trac.macports.org/ticket/38409> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #38401: new port: py-khmer
by MacPorts 17 Mar '13

17 Mar '13

#38401: new port: py-khmer ------------------------+-------------------------------- Reporter: sean@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: ------------------------+-------------------------------- -- Ticket URL: <https://trac.macports.org/ticket/38401> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #38397: new port: bowtie2
by MacPorts 16 Mar '13

16 Mar '13

#38397: new port: bowtie2 ------------------------+-------------------------------- Reporter: sean@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: | Port: ------------------------+-------------------------------- -- Ticket URL: <https://trac.macports.org/ticket/38397> MacPorts <http://www.macports.org/> Ports system for OS X

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