package-announce November 2011

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Fedora 15 Update: R-biomaRt-2.10.0-1.fc15
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-biomaRt Product : Fedora 15 Version : 2.10.0 Release : 1.fc15 URL : http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html Summary : R Interface to BioMart databases Description : In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining. -------------------------------------------------------------------------------- Update Information: Update R to 2.14.0. This required a mass rebuild of R components. -------------------------------------------------------------------------------- References: [ 1 ] Bug #751003 - New version of R 2.14.0 is available https://bugzilla.redhat.com/show_bug.cgi?id=751003 [ 2 ] Bug #753188 - Review Request: R-rtracklayer - R interface to genome browsers and their annotation tracks https://bugzilla.redhat.com/show_bug.cgi?id=753188 [ 3 ] Bug #753181 - Review Request: R-RCurl - General network (HTTP/FTP) client interface for R https://bugzilla.redhat.com/show_bug.cgi?id=753181 [ 4 ] Bug #753182 - Review Request: R-biomaRt - R Interface to BioMart databases https://bugzilla.redhat.com/show_bug.cgi?id=753182 [ 5 ] Bug #753185 - Review Request: R-Rcompression - R Package for in-memory compression https://bugzilla.redhat.com/show_bug.cgi?id=753185 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update R-biomaRt' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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Fedora 15 Update: R-GenomicFeatures-1.6.1-1.fc15
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-GenomicFeatures Product : Fedora 15 Version : 1.6.1 Release : 1.fc15 URL : http://bioconductor.org/packages/2.9/bioc/html/GenomicFeatures.html Summary : Tools for making and manipulating transcript centric annotations Description : A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format. -------------------------------------------------------------------------------- Update Information: Update R to 2.14.0. This required a mass rebuild of R components. -------------------------------------------------------------------------------- ChangeLog: * Wed Nov 9 2011 Tom Callaway <spot(a)fedoraproject.org> - 1.6.1-1 - update to 1.6.1 -------------------------------------------------------------------------------- References: [ 1 ] Bug #751003 - New version of R 2.14.0 is available https://bugzilla.redhat.com/show_bug.cgi?id=751003 [ 2 ] Bug #753188 - Review Request: R-rtracklayer - R interface to genome browsers and their annotation tracks https://bugzilla.redhat.com/show_bug.cgi?id=753188 [ 3 ] Bug #753181 - Review Request: R-RCurl - General network (HTTP/FTP) client interface for R https://bugzilla.redhat.com/show_bug.cgi?id=753181 [ 4 ] Bug #753182 - Review Request: R-biomaRt - R Interface to BioMart databases https://bugzilla.redhat.com/show_bug.cgi?id=753182 [ 5 ] Bug #753185 - Review Request: R-Rcompression - R Package for in-memory compression https://bugzilla.redhat.com/show_bug.cgi?id=753185 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update R-GenomicFeatures' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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[SECURITY] Fedora 15 Update: ReviewBoard-1.5.7-1.fc15
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15933 2011-11-15 23:41:10 -------------------------------------------------------------------------------- Name : ReviewBoard Product : Fedora 15 Version : 1.5.7 Release : 1.fc15 URL : http://www.review-board.org Summary : Web-based code review tool Description : Review Board is a powerful web-based code review tool that offers developers an easy way to handle code reviews. It scales well from small projects to large companies and offers a variety of tools to take much of the stress and time out of the code review process. -------------------------------------------------------------------------------- Update Information: - New upstream security release 1.5.7 - Security Fixes: - A script injection vulnerability was discovered in the commenting system. This affected the diff viewer and screenshot pages, and allowed a commenter to break the page and execute JavaScript -------------------------------------------------------------------------------- ChangeLog: * Tue Nov 15 2011 Stephen Gallagher <sgallagh(a)redhat.com> - 1.5.7-1 - New upstream security release 1.5.7 - Security Fixes: - A script injection vulnerability was discovered in the commenting system. This affected the diff viewer and screenshot pages, and allowed a commenter to break the page and execute JavaScript * Mon Aug 22 2011 Stephen Gallagher <sgallagh(a)redhat.com> - 1.5.6-1 - New upstream release 1.5.6 - http://www.reviewboard.org/docs/releasenotes/dev/reviewboard/1.5.6/ - New Features: - The PATH environment variable is now shown in the error when patch.exe can't be found, in order to help figure out where it needs to go - rb-site more clearly informs that an existing database with valid permissions is needed for installation - rb-site now lists recommendations for different services, and lists options that aren’t officially supported - Tabs in the diff viewer are now marked up, allowing custom stylesheets to display them differently. By default, they don’t look any different - Added Fedora Hosted to the hosting provider options - Editing a field and then canceling it on a review request now prompts for confirmation before discarding the new text - Control-S now saves the current text in review request fields - We now support storing lots of text in the Description and Testing Done fields on MySQL - Performance Improvements: - Review Board now requires Pygments 1.4 or higher. Older installations running older versions of Pygments should get a performance increase when rendering diffs - Bug Fixes: - Using Review Board with wsgi without mod_python installed on the system no longer prevents Review Board from breaking - Screenshot draft captions are now always displayed correctly. Previously, only the main caption would display, making them appear blank on new uploads - Changing screenshot draft captions now invalidates the cache, allowing them to be seen when reloading the page - When sending an e-mail, we no longer crash if the sender has no e-mail address - Caching really long files or diffs now works more consistently. Previously, it was possible for the data to not be stored correctly - Fixed a date range calculation sometimes causing the log viewer to fail on the first of the month - Failing to load the Review Board News feed in the administration UI due to a proxy will no longer cause an HTTP 500 error to display - Invalid bug tracker URLs (those containing more than one %s, for example) in the administration UI no longer breaks review requests - The Mercurial support no longer overrides the SSH client configuration if one is already provided - The recaptcha_client dependency has been renamed to recaptcha-client. Both technically work, but the former is more correct and makes packaging easier - Fixed a few occasional errors that could show up on the dashboard under certain conditions * Fri Jun 17 2011 Stephen Gallagher <sgallagh(a)redhat.com> - 1.5.5-2 - Resolves: rhbz#598463 - rb-site suggest that I use an unsafe temporary - directory -------------------------------------------------------------------------------- References: [ 1 ] Bug #754130 - CVE-2011-4312 ReviewBoard: XSS in the commenting system (diff viewer and screenshot pages) [fedora-all] https://bugzilla.redhat.com/show_bug.cgi?id=754130 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update ReviewBoard' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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Fedora 16 Update: tomcat-7.0.22-2.fc16
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15815 2011-11-12 03:06:10 -------------------------------------------------------------------------------- Name : tomcat Product : Fedora 16 Version : 7.0.22 Release : 2.fc16 URL : http://tomcat.apache.org/ Summary : Apache Servlet/JSP Engine, RI for Servlet 3.0/JSP 2.2 API Description : Tomcat is the servlet container that is used in the official Reference Implementation for the Java Servlet and JavaServer Pages technologies. The Java Servlet and JavaServer Pages specifications are developed by Sun under the Java Community Process. Tomcat is developed in an open and participatory environment and released under the Apache Software License version 2.0. Tomcat is intended to be a collaboration of the best-of-breed developers from around the world. -------------------------------------------------------------------------------- Update Information: - Move tomcat-juli.jar to lib package - Drop %%update_maven_depmap as in tomcat6 - Provide native systemd unit file ported from tomcat6 -------------------------------------------------------------------------------- ChangeLog: * Fri Nov 11 2011 Ivan Afonichev <ivan.afonichev(a)gmail.com> 0:7.0.22-2 - Move tomcat-juli.jar to lib package - Drop %update_maven_depmap as in tomcat6 - Provide native systemd unit file ported from tomcat6 -------------------------------------------------------------------------------- References: [ 1 ] Bug #752571 - Packaging Juli logging jar under tomcat-lib https://bugzilla.redhat.com/show_bug.cgi?id=752571 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update tomcat' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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Fedora 16 Update: allegro-4.4.2-2.fc16
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-16009 2011-11-17 22:46:04 -------------------------------------------------------------------------------- Name : allegro Product : Fedora 16 Version : 4.4.2 Release : 2.fc16 URL : http://alleg.sourceforge.net/ Summary : A game programming library Description : Allegro is a cross-platform library intended for use in computer games and other types of multimedia programming. -------------------------------------------------------------------------------- Update Information: Fix pre/post dependencies for non ix86 arches including x86_64 and ARM -------------------------------------------------------------------------------- ChangeLog: * Tue Nov 15 2011 Peter Robinson <pbrobinson(a)fedoraproject.org> 4.4.2-2 - Make pre/post dependencies for all non i686 arches sane -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update allegro' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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Fedora 16 Update: mcelog-1.0-0.3.6e4e2a00.fc16
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-16129 2011-11-19 05:17:23 -------------------------------------------------------------------------------- Name : mcelog Product : Fedora 16 Version : 1.0 Release : 0.3.6e4e2a00.fc16 URL : https://github.com/andikleen/mcelog.git Summary : Tool to translate x86-64 CPU Machine Check Exception data. Description : mcelog is a utility that collects and decodes Machine Check Exception data on x86-32 and x86-64 systems. It can be run either as a daemon, or by cron. -------------------------------------------------------------------------------- Update Information: - Updated sources to deal with various warning issues [701083] [704302] - Update URL for new location of Andi's mcelog tree - Update n-v-r to include latest git hash -------------------------------------------------------------------------------- ChangeLog: * Thu Nov 17 2011 Prarit Bhargava <prarit(a)redhat.com> 2:1.0-0.3.6e4e2a00 - Updated sources to deal with various warning issues [701083] [704302] - Update URL for new location of Andi's mcelog tree - Update n-v-r to include latest git hash -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update mcelog' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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[SECURITY] Fedora 15 Update: libsocialweb-0.25.20-1.fc15
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15839 2011-11-13 04:38:51 -------------------------------------------------------------------------------- Name : libsocialweb Product : Fedora 15 Version : 0.25.20 Release : 1.fc15 URL : http://www.gnome.org/ Summary : A social network data aggregator Description : libsocialweb is a social data server which fetches data from the "social web", such as your friend's blog posts and photos, upcoming events, recently played tracks, and pending eBay* auctions. It also provides a service to update your status on web services which support it, such as MySpace* and Twitter*. -------------------------------------------------------------------------------- Update Information: CVE-2011-4129 A security flaw was found in the way the libsocialweb, a social network data aggregator, performed its initialization when this service start was initiated by the dbus daemon. Due to a deficiency in a way the libsocialweb service was initialized, an untrusted (non-SSL) network connection has been opened to remote Twitter service servers without explicit approval of the user, running the libsocialweb service on the local host. A remote attacker could use this flaw to conduct various MITM attacks and potentially alter integrity of the user account in question. * libsocialweb: The views will try and fetch content from the web service even if they aren't configured. * rest: enforce that the SSL certificate is valid -------------------------------------------------------------------------------- ChangeLog: * Sat Nov 12 2011 Peter Robinson <pbrobinson(a)fedoraproject.org> 0.25.20-1 - update to 0.25.20. Fixes CVE-2011-4129, RHBZ 752022 * Mon Jul 4 2011 Bastien Nocera <bnocera(a)redhat.com> 0.25.19-1 - Update to 0.25.19 * Wed Jun 15 2011 Peter Robinson <pbrobinson(a)fedoraproject.org> 0.25.18-1 - Update to 0.25.18 * Sun May 22 2011 Peter Robinson <pbrobinson(a)fedoraproject.org> 0.25.17-1 - Update to 0.25.17 -------------------------------------------------------------------------------- References: [ 1 ] Bug #752022 - CVE-2011-4129 libsocialweb: Untrusted connection to Twitter without user's approval upon service start via dbus https://bugzilla.redhat.com/show_bug.cgi?id=752022 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update libsocialweb' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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[SECURITY] Fedora 15 Update: rest-0.7.12-1.fc15
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15839 2011-11-13 04:38:51 -------------------------------------------------------------------------------- Name : rest Product : Fedora 15 Version : 0.7.12 Release : 1.fc15 URL : http://www.gnome.org Summary : A library for access to RESTful web services Description : This library was designed to make it easier to access web services that claim to be "RESTful". A RESTful service should have urls that represent remote objects, which methods can then be called on. The majority of services don't actually adhere to this strict definition. Instead, their RESTful end point usually has an API that is just simpler to use compared to other types of APIs they may support (XML-RPC, for instance). It is this kind of API that this library is attempting to support. -------------------------------------------------------------------------------- Update Information: CVE-2011-4129 A security flaw was found in the way the libsocialweb, a social network data aggregator, performed its initialization when this service start was initiated by the dbus daemon. Due to a deficiency in a way the libsocialweb service was initialized, an untrusted (non-SSL) network connection has been opened to remote Twitter service servers without explicit approval of the user, running the libsocialweb service on the local host. A remote attacker could use this flaw to conduct various MITM attacks and potentially alter integrity of the user account in question. * libsocialweb: The views will try and fetch content from the web service even if they aren't configured. * rest: enforce that the SSL certificate is valid -------------------------------------------------------------------------------- ChangeLog: * Thu Nov 10 2011 Peter Robinson <pbrobinson(a)fedoraproject.org> 0.7.12-1 - Release 0.7.12. Fixes CVE-2011-4129 RHBZ 752022 * Fri Oct 28 2011 Peter Robinson <pbrobinson(a)fedoraproject.org> 0.7.11-1 - Release 0.7.11 -------------------------------------------------------------------------------- References: [ 1 ] Bug #752022 - CVE-2011-4129 libsocialweb: Untrusted connection to Twitter without user's approval upon service start via dbus https://bugzilla.redhat.com/show_bug.cgi?id=752022 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update rest' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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Fedora 16 Update: groovy-1.8.4-1.fc16
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-16185 2011-11-20 23:36:09 -------------------------------------------------------------------------------- Name : groovy Product : Fedora 16 Version : 1.8.4 Release : 1.fc16 URL : http://groovy.codehaus.org/ Summary : Dynamic language for the Java Platform Description : Groovy is an agile and dynamic language for the Java Virtual Machine, built upon Java with features inspired by languages like Python, Ruby and Smalltalk. It seamlessly integrates with all existing Java objects and libraries and compiles straight to Java bytecode so you can use it anywhere you can use Java. -------------------------------------------------------------------------------- Update Information: Update to recent upstream version which fixes some bugs and includes some enhancements. Further information could be found: http://jira.codehaus.org/secure/ReleaseNote.jspa?projectId=10242&version=17… -------------------------------------------------------------------------------- ChangeLog: * Sun Nov 20 2011 Johannes Lips <hannes(a)fedoraproject.org> - 1.8.4-1 - Update to 1.8.4 -------------------------------------------------------------------------------- References: [ 1 ] Bug #753111 - groovy-1.8.4 is available https://bugzilla.redhat.com/show_bug.cgi?id=753111 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update groovy' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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Fedora 15 Update: python-flask-0.6.1-3.fc15
by updates＠fedoraproject.org 29 Nov '11

29 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-16027 2011-11-17 22:47:08 -------------------------------------------------------------------------------- Name : python-flask Product : Fedora 15 Version : 0.6.1 Release : 3.fc15 URL : http://flask.pocoo.org/ Summary : A micro-framework for Python based on Werkzeug, Jinja 2 and good intentions Description : Flask is called a “micro-framework” because the idea to keep the core simple but extensible. There is no database abstraction layer, no form validation or anything else where different libraries already exist that can handle that. However Flask knows the concept of extensions that can add this functionality into your application as if it was implemented in Flask itself. There are currently extensions for object relational mappers, form validation, upload handling, various open authentication technologies and more. -------------------------------------------------------------------------------- Update Information: Fixes bug regarding ownership of easy-install.pth -------------------------------------------------------------------------------- ChangeLog: * Wed Nov 16 2011 Dan Young <dyoung(a)mesd.k12.or.us> - 0.6.1-3 - don't own easy-install.pth -------------------------------------------------------------------------------- References: [ 1 ] Bug #752706 - python-flask breaks locally installed eggs by containing bogus easy-install.pth https://bugzilla.redhat.com/show_bug.cgi?id=752706 -------------------------------------------------------------------------------- This update can be installed with the "yum" update program. Use su -c 'yum update python-flask' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/. All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------

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package-announce November 2011