June 2015 - macports-tickets - lists.macosforge.org

[MacPorts] #48054: py-pbspy: Incorrect permissions on [..]/site-packages/obspy/taup/data
by MacPorts 17 Jun '15

17 Jun '15

#48054: py-pbspy: Incorrect permissions on [..]/site-packages/obspy/taup/data ----------------------------+-------------------------------- Reporter: andy.nowacki@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: py-obspy ----------------------------+-------------------------------- ObsPy (as of trunk r137599) has a problem with file permissions. Specifically, the code requires read access to the following files and directories by a normal user, but they are currently set as readable only by root:wheel: 1. ${prefix}/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy-0.10.2-py2.7.egg-info {{{ $ ls -l /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy-0.10.2-py2.7.egg-info/ total 160 -rw------- 1 root wheel 2611 19 May 20:28 PKG-INFO -rw------- 1 root wheel 47494 19 May 20:28 SOURCES.txt -rw------- 1 root wheel 1 19 May 20:28 dependency_links.txt -rw------- 1 root wheel 7552 19 May 20:28 entry_points.txt -rw------- 1 root wheel 1 19 May 20:28 namespace_packages.txt -rw------- 1 root wheel 1 15 May 19:36 not-zip-safe -rw------- 1 root wheel 141 19 May 20:28 requires.txt -rw------- 1 root wheel 166 19 May 20:28 top_level.txt }}} This directory sometimes itself lacks execution permission for all users, but I could not reliably reproduce this when uninstalling and installing ObsPy to test. 2. ${prefix}/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/data {{{ $ ls -l /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/data total 616 -rw------- 1 root wheel 81 15 May 19:31 README.txt -rw------- 1 root wheel 144910 15 May 19:31 ak135.npz -rw------- 1 root wheel 6413 15 May 19:31 ak135.tvel -rw------- 1 root wheel 145978 15 May 19:31 iasp91.npz -rw------- 1 root wheel 5761 15 May 19:31 iasp91.tvel }}} The code below shows both the errors and my interim fix. {{{ $ cat /tmp/test.py from obspy.taup import TauPyModel m = TauPyModel() $ $ python2.7 /tmp/test.py && echo success Traceback (most recent call last): File "/tmp/test.py", line 1, in <module> from obspy.taup import TauPyModel File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/__init__.py", line 36, in <module> from obspy.core.utcdatetime import UTCDateTime # NOQA File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/core/__init__.py", line 107, in <module> from obspy.core.util.attribdict import AttribDict File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/core/util/__init__.py", line 40, in <module> from obspy.core.util.obspy_types import (ComplexWithUncertainties, Enum, File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/core/util/obspy_types.py", line 16, in <module> with standard_library.hooks(): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/future/standard_library/__init__.py", line 323, in __enter__ install_hooks() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/future/standard_library/__init__.py", line 528, in install_hooks install_aliases() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/future/standard_library/__init__.py", line 482, in install_aliases import test File "/private/tmp/test.py", line 2, in <module> m = TauPyModel() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/tau.py", line 317, in __init__ self.model = TauModel.from_file(model) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/tau_model.py", line 600, in from_file return TauModel.deserialize(filename) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/tau_model.py", line 520, in deserialize npz = np.load(filename) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/lib/npyio.py", line 369, in load fid = open(file, "rb") IOError: [Errno 13] Permission denied: u'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/data/iasp91.npz' $ $ sudo chmod a+r /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy-0.10.2-py2.7.egg-info/* $ python2.7 /tmp/test.py && echo success Traceback (most recent call last): File "/tmp/test.py", line 1, in <module> from obspy.taup import TauPyModel File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/__init__.py", line 36, in <module> from obspy.core.utcdatetime import UTCDateTime # NOQA File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/core/__init__.py", line 107, in <module> from obspy.core.util.attribdict import AttribDict File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/core/util/__init__.py", line 40, in <module> from obspy.core.util.obspy_types import (ComplexWithUncertainties, Enum, File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/core/util/obspy_types.py", line 16, in <module> with standard_library.hooks(): File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/future/standard_library/__init__.py", line 323, in __enter__ install_hooks() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/future/standard_library/__init__.py", line 528, in install_hooks install_aliases() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/future/standard_library/__init__.py", line 482, in install_aliases import test File "/private/tmp/test.py", line 2, in <module> m = TauPyModel() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/tau.py", line 317, in __init__ self.model = TauModel.from_file(model) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/tau_model.py", line 600, in from_file return TauModel.deserialize(filename) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/tau_model.py", line 520, in deserialize npz = np.load(filename) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/numpy/lib/npyio.py", line 369, in load fid = open(file, "rb") IOError: [Errno 13] Permission denied: u'/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/data/iasp91.npz' $ $ sudo chmod a+x /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/data $ sudo chmod a+r /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7 /site-packages/obspy/taup/data/* $ python2.7 /tmp/test.py && echo success success }}} My apologies for not presenting a patch to fix this, but I doubt that just adding the chmod commands would be a satisfactory fix. -- Ticket URL: <https://trac.macports.org/ticket/48054> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48086: mpich subports use -devel suffix incorrectly
by MacPorts 17 Jun '15

17 Jun '15

#48086: mpich subports use -devel suffix incorrectly --------------------------+------------------------ Reporter: ryandesign@… | Owner: eborisch@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.99 Keywords: | Port: mpich --------------------------+------------------------ The mpich port's subports use the -devel suffix incorrectly. The correct way is that the set of files installed by a port (e.g. mpich- gcc5) is more or less identical to the set of files installed by its -devel counterpart (e.g. mpich-devel-gcc5), and that because the ports install the same files to the same places, the ports are marked as conflicting with one another. The ports are thus interchangeable. For example, a user can deactivate mpich-gcc5 and install mpich-devel-gcc5, and any ports declaring dependencies on mpich-gcc5 using a path:-style dependency will still work. Documentation about -devel ports is pending but see #14540 for a basic description of the expectations. This is not how the mpich subports currently work. In fact e.g. mpich-gcc5 and mpich-devel-gcc5 do not have any files in common at all, and they can be installed simultaneously. This is specifically not desired in this case, and should be corrected so that -devel and non-devel ports install the same files and conflict. This also means that the -devel ports should present themselves under the non-devel name in the "port select" interface. -- Ticket URL: <https://trac.macports.org/ticket/48086> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48049: verbiste @0.1.41
by MacPorts 17 Jun '15

17 Jun '15

#48049: verbiste @0.1.41 -----------------------------+-------------------------------- Reporter: geekpourjesus@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: verbiste -----------------------------+-------------------------------- -- Ticket URL: <https://trac.macports.org/ticket/48049> MacPorts <https://www.macports.org/> Ports system for OS X

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Re: [MacPorts] #44500: gdb @7.7.1_1: update to 7.9.1
by MacPorts 17 Jun '15

17 Jun '15

#44500: gdb @7.7.1_1: update to 7.9.1 --------------------------------+------------------------------- Reporter: cartasegna.luca@… | Owner: stuartwesterman@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch Port: gdb | --------------------------------+------------------------------- Comment (by stuartwesterman@…): I've attached the diff with the revision line taken out. -- Ticket URL: <https://trac.macports.org/ticket/44500#comment:10> MacPorts <https://www.macports.org/> Ports system for OS X

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Re: [MacPorts] #44500: gdb @7.7.1_1: update to 7.9.1
by MacPorts 17 Jun '15

17 Jun '15

#44500: gdb @7.7.1_1: update to 7.9.1 --------------------------------+------------------------------- Reporter: cartasegna.luca@… | Owner: stuartwesterman@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: haspatch Port: gdb | --------------------------------+------------------------------- Comment (by mf2k@…): Thanks. The {{{revision}}} line should be deleted because it starts at 0 when increasing the version and that is the default value. -- Ticket URL: <https://trac.macports.org/ticket/44500#comment:9> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48064: py27-astropy fails in build stage on G4 running Leopard 10.5.8
by MacPorts 17 Jun '15

17 Jun '15

#48064: py27-astropy fails in build stage on G4 running Leopard 10.5.8 -------------------------------------------------+------------------------- Reporter: zanderpower@… | Owner: macports- Type: defect | tickets@… Priority: Normal | Status: new Component: ports | Milestone: Keywords: leopard "read_only_relocs suppress" | Version: 2.3.3 | Port: | py27-astropy -------------------------------------------------+------------------------- The error message is {{{ :info:build ld: absolute addressing (perhaps -mdynamic-no-pic) used in _celini from /mp2/local/lib/libwcs.a(cel.o) not allowed in slidable image. Use '-read_only_relocs suppress' to enable text relocs :info:build collect2: ld returned 1 exit status :info:build error: command '/usr/bin/gcc-4.2' failed with exit status 1 :info:build Command failed: cd "/mp2/local/var/macports/build/ }}} However, it builds and installs without error if I comment out the line {{{ --use-system-wcslib }}} in its Portfile. I am fairly confident that this is related to the way I installed wcslib: as wcslib failed in the destroot phase, I added the line {{{ configure.ldflags-append "read_only_relocs suppress" }}} to _its_ Portfile. See ticket #48047. Note that py27-astropy fails with the same error as wcslib did. I tried adding "read_only_relocs suppress" to py27-astropy's Portfile, but no luck. -- Ticket URL: <https://trac.macports.org/ticket/48064> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #47745: nghttp2 @0.7.14_0: update to version 1.0.0
by MacPorts 17 Jun '15

17 Jun '15

#47745: nghttp2 @0.7.14_0: update to version 1.0.0 ---------------------------------+-------------------------------- Reporter: mschamschula@… | Owner: macports-tickets@… Type: update | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: haspatch maintainer | Port: nghttp2 ---------------------------------+-------------------------------- nghttp2 has been updated to version 1.0.0: {{{ Implements RFC 7540 HTTP/2 (https://tools.ietf.org/html/rfc7540) implements RFC 7541 HPACK (https://tools.ietf.org/html/rfc7541) v1.0.0 introduced backward incompatible changes from 0.7 series. Read https://nghttp2.org/documentation/package_README.html#migration- from-v0-7-15-or-earlier to migrate from older version to this latest version. }}} -- Ticket URL: <https://trac.macports.org/ticket/47745> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #47288: sbcl @1.2.9 fails building on a 10.5.8 PPC
by MacPorts 17 Jun '15

17 Jun '15

#47288: sbcl @1.2.9 fails building on a 10.5.8 PPC ------------------------+-------------------------------- Reporter: braumann@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: sbcl ------------------------+-------------------------------- I have tried to install {{{sbcl @1.2.9}}} in order to install {{{maxima}}} later on, however, after a long time {{{sbcl}}} building fails. As I never ever have used LISP before I am not able to interpret the log file, sorry. I attach the main.log -- Ticket URL: <https://trac.macports.org/ticket/47288> MacPorts <https://www.macports.org/> Ports system for OS X

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Re: [MacPorts] #40259: postgis2 @2.0.3_0 Won't install alongside Postgis 1.5 even in a separate PostgreSQL
by MacPorts 17 Jun '15

17 Jun '15

#40259: postgis2 @2.0.3_0 Won't install alongside Postgis 1.5 even in a separate PostgreSQL -------------------------------+--------------------- Reporter: jea@… | Owner: vince@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.2.0 Resolution: fixed | Keywords: Port: postgis postgis2 | -------------------------------+--------------------- Comment (by vince@…): Yeah, that’s because proj has been upgraded as part of your postgis2 install, so the dylib version has bumped. -- Ticket URL: <https://trac.macports.org/ticket/40259#comment:9> MacPorts <https://www.macports.org/> Ports system for OS X

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[MacPorts] #48069: libxslt fails to fetch
by MacPorts 17 Jun '15

17 Jun '15

#48069: libxslt fails to fetch ----------------------------+-------------------------------- Reporter: bonsaiviking@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Keywords: | Port: libxslt ----------------------------+-------------------------------- libxslt's Portfile refers to a missing patch file. Commenting out the patchfiles-append directive allows installation to continue. {{{ ~/macports-10.8/ports$ port upgrade outdated ---> Computing dependencies for libxslt ---> Fetching distfiles for libxslt ---> Attempting to fetch yosemite-libtool.patch from http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://distfiles.macports.org/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://sea.us.distfiles.macports.org/macports/distfiles/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://lil.fr.distfiles.macports.org/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://xmlsoft.org/sources/ ---> Attempting to fetch yosemite-libtool.patch from ftp://xmlsoft.org/libxslt/ ---> Attempting to fetch yosemite-libtool.patch from http://mse.uk.distfiles.macports.org/sites/distfiles.macports.org/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://nue.de.distfiles.macports.org/macports/distfiles/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://fco.it.distfiles.macports.org/mirrors/macports-distfiles/libxslt ---> Attempting to fetch yosemite-libtool.patch from ftp://gd.tuwien.ac.at/pub/libxml/ ---> Attempting to fetch yosemite-libtool.patch from http://osl.no.distfiles.macports.org/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://cjj.kr.distfiles.macports.org/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://her.gr.distfiles.macports.org/mirrors/macports/mpdistfiles/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/libxslt ---> Attempting to fetch yosemite-libtool.patch from http://jog.id.distfiles.macports.org/macports/mpdistfiles/libxslt ---> Attempting to fetch yosemite-libtool.patch from ftp://fr.rpmfind.net/pub/libxml/ ---> Attempting to fetch yosemite-libtool.patch from http://svn.macports.org/repository/macports/distfiles/libxslt Error: org.macports.fetch for port libxslt returned: fetch failed Please see the log file for port libxslt for details: /Users/david/macports-10.8/var/macports/logs/_Users_david_macports-10.8_ports_textproc_libxslt/libxslt/main.log Error: Unable to upgrade port: 1 }}} -- Ticket URL: <https://trac.macports.org/ticket/48069> MacPorts <https://www.macports.org/> Ports system for OS X

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