September 2014 - macports-tickets - lists.macosforge.org

[MacPorts] #42383: emacs-app: apply patch against distnoted leak
by MacPorts 27 Sep '14

27 Sep '14

#42383: emacs-app: apply patch against distnoted leak -----------------------------+-------------------------------- Reporter: akim.demaille@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: emacs-app -----------------------------+-------------------------------- Hi! On my Mavericks, I face the issue describe in various places (http://apple.stackexchange.com/questions/111197/runaway-distnoted- process, https://discussions.apple.com/message/24709817#24709817) the current version of Emacs causes distnoted to eat a lot of CPU (100% of a core), and a lot of RAM (1.5GB+). Someone posted a patch here: https://gist.github.com/anonymous/8553178 According to this page, this very patch will be part of 24.4. In the meanwhile, it would be really nice if MacPorts' emacs-app could apply the fix locally. Cheers! -- Ticket URL: <https://trac.macports.org/ticket/42383> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #43431: Ports with a mysql5 variants and/or dependencies should switch to using mysql56 or possibly mariadb.
by MacPorts 27 Sep '14

27 Sep '14

#43431: Ports with a mysql5 variants and/or dependencies should switch to using mysql56 or possibly mariadb. -------------------------+-------------------------------- Reporter: pixilla@… | Owner: macports-tickets@… Type: enhancement | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.2.1 Keywords: | Port: -------------------------+-------------------------------- The following ports have variants and/or dependencies on mysql5: {{{ aqua/qt3-mac aqua/qt4-mac-mysql55-plugin databases/dbslayer databases/libdbi-drivers databases/libgda4 databases/libgda5 databases/libzdb-mysql55 databases/mysql-connector-odbc databases/mysql5 databases/mysql55-connector-cpp databases/mysql55-lib_mysqludf_json databases/mysqlxx databases/ocaml-mysql databases/soci devel/akonadi devel/apr-util devel/bugzilla devel/pficommon devel/radlib games/pennmush gis/gdal gis/grass gnome/libgda graphics/vtk-devel kde/amarok-devel lang/neko lang/php lang/php4 lang/php52 lang/qore-mysql-module mail/dbmail mail/dovecot mail/dovecot2 mail/dspam mail/exim mail/postfix mail/postfix-devel mail/vpopmail net/flow-tools net/mediatomb net/nagios-plugins net/proftpd net/pure-ftpd net/restund net/snort net/zabbix net/zabbix2 perl/p5-dbd-mysql perl/p5-dbd-mysql5 php/php5-mysql python/py-mysql python/py-oursql ruby/rb-mysql ruby/rb19-mysql security/hydra sysutils/freeradius textproc/sphinx www/drupal5 www/drupal6 www/lighttpd www/lighttpd-devel www/mnogosearch www/redland www/wikkawiki }}} -- Ticket URL: <https://trac.macports.org/ticket/43431> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #45173: Upgrade bash to 4.3.26
by MacPorts 27 Sep '14

27 Sep '14

#45173: Upgrade bash to 4.3.26 ------------------------+-------------------------------- Reporter: hahn.seb@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Keywords: haspatch | Port: bash ------------------------+-------------------------------- Fixes CVE 2014-7169 -- Ticket URL: <https://trac.macports.org/ticket/45173> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #45172: Unable to upgrade port 1
by MacPorts 27 Sep '14

27 Sep '14

#45172: Unable to upgrade port 1 ----------------------------+-------------------------------- Reporter: marciods2003@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Keywords: cmake update | Port: cmake ----------------------------+-------------------------------- sh-3.2# port upgrade outdated ---> Computing dependencies for cmake ---> Configuring cmake Error: org.macports.configure for port cmake returned: configure failure: command execution failed Please see the log file for port cmake for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_devel_cmake/cmake/main.log Error: Unable to upgrade port: 1 To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets -- Ticket URL: <https://trac.macports.org/ticket/45172> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #45171: Processing of port toilet failed
by MacPorts 27 Sep '14

27 Sep '14

#45171: Processing of port toilet failed ----------------------------+-------------------------------- Reporter: marciods2003@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Keywords: libcaca | Port: toilet ----------------------------+-------------------------------- Error: org.macports.build for port libcaca returned: command execution failed Error: Failed to install libcaca Please see the log file for port libcaca for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_libcaca/libcaca/main.log Error: The following dependencies were not installed: libcaca To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port toilet failed -- Ticket URL: <https://trac.macports.org/ticket/45171> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #45163: Prokka fails to build (some macports were used for the dependencies)
by MacPorts 26 Sep '14

26 Sep '14

#45163: Prokka fails to build (some macports were used for the dependencies) -------------------------+-------------------------------- Reporter: hobbsilla@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Keywords: | Port: -------------------------+-------------------------------- I attempted to build my prokka database and get this abort message. Could someone help me figure out based on the provide output from my terminal where I could find a more detailed log that I could attach to this ticket? I used CPAN to install Bioperl. I believe cpanminus is in the macports but I'm not sure if I managed to install CPAN from elsewhere. I have ncbi_tools macports installed plus the blast+ through the source code just to cover my bases. I install GNU Parallel through the Macports. All of the other dependencies I installed from source code (HMMER, Aragorn, Prodigal and Infernal). Any help would be greatly appreciated. {{{ $ prokka --setupdb Can't locate XML/Simple.pm in @INC (@INC contains: /opt/local/lib/perl5/site_perl/5.12.5/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.12.5 /opt/local/lib/perl5/vendor_perl/5.12.5/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.12.5 /opt/local/lib/perl5/5.12.5 /darwin-thread-multi-2level /opt/local/lib/perl5/5.12.5 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl/5.12.4 /darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.12.4 /opt/local/lib/perl5/vendor_perl .) at /Users/elixir/Documents/Programming_Folder/bioinfo/prokka-1.10/bin/prokka line 25. }}} -- Ticket URL: <https://trac.macports.org/ticket/45163> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #45114: Erlang can't load crypto library
by MacPorts 26 Sep '14

26 Sep '14

#45114: Erlang can't load crypto library ----------------------+------------------------------------- Reporter: dedalo@… | Owner: macports-tickets@… Type: defect | Status: new Priority: High | Milestone: Component: ports | Version: 2.3.1 Keywords: | Port: erlang @17.3_0+hipe+ssl ----------------------+------------------------------------- There is a problem with the openssl library. When I try to load the crypto library, which depends on ssl, an exception is triggered. I'm on Mac OS X 10.7.5. erl Erlang/OTP 17 [erts-6.2] [source] [64-bit] [smp:4:4] [async-threads:10] [hipe] [kernel-poll:false] Eshell V6.2 (abort with ^G) 1> crypto:start(). ** exception error: undefined function crypto:start/0 2> =ERROR REPORT==== 21-Sep-2014::17:55:32 === Unable to load crypto library. Failed with error: "load, Library load-call unsuccessful." OpenSSL might not be installed on this system. =ERROR REPORT==== 21-Sep-2014::17:55:32 === The on_load function for module crypto returned {error, {load, "Library load-call unsuccessful."}} port installed erlang The following ports are currently installed: erlang @17.1_0+hipe+ssl erlang @17.3_0+hipe+ssl (active) -- Ticket URL: <https://trac.macports.org/ticket/45114> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #45161: [NEW] oclint
by MacPorts 26 Sep '14

26 Sep '14

#45161: [NEW] oclint ------------------------+-------------------------------- Reporter: adexter@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Keywords: | Port: oclint ------------------------+-------------------------------- -- Ticket URL: <https://trac.macports.org/ticket/45161> MacPorts <http://www.macports.org/> Ports system for OS X

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[MacPorts] #36812: new port: pocketsphinx 0.7
by MacPorts 26 Sep '14

26 Sep '14

#36812: new port: pocketsphinx 0.7 ------------------------+-------------------------------- Reporter: qqshfox@… | Owner: macports-tickets@… Type: submission | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Keywords: | Port: pocketsphinx ------------------------+-------------------------------- Another speech recognition system from CMU. -- Ticket URL: <https://trac.macports.org/ticket/36812> MacPorts <http://www.macports.org/> Ports system for Mac OS

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[MacPorts] #45147: mediawiki depends on obsolete php5-dba
by MacPorts 26 Sep '14

26 Sep '14

#45147: mediawiki depends on obsolete php5-dba -------------------------+-------------------------------- Reporter: n.gilbert@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.1 Keywords: | Port: -------------------------+-------------------------------- Trying to install mediawiki, port lists the dependencies as including php5-dba, but that generates an error (see below). bash-3.2# port install mediawiki ---> Computing dependencies for mediawiki ---> Dependencies to be installed: php5-dba php5-intl php5-mbstring php5-mysql php5-web php5 ---> Configuring php5-dba Error: php5-dba has been made obsolete by the port php53-dba. Please install php53-dba instead. Error: org.macports.configure for port php5-dba returned: obsolete port Error: Failed to install php5-dba Please see the log file for port php5-dba for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_php_php5-dba/php5-dba/main.log Error: The following dependencies were not installed: php5-dba php5-intl php5-mbstring php5-mysql php5-web php5 To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port mediawiki failed Installing php53-dba first does not help (and anyway the current version of php-dba is php56-dba). -- Ticket URL: <https://trac.macports.org/ticket/45147> MacPorts <http://www.macports.org/> Ports system for OS X

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