package-announce November 2011

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Fedora 15 Update: R-multtest-2.10.0-2.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-multtest Product : Fedora 15 Version : 2.10.0 Release : 2.fc15 URL : http://www.bioconductor.org/packages/release/bioc/html/multtest.html Summary : Multiple hypothesis testing library from Bioconductor Description : Non-parametric bootstrap and permutation resampling-based multiple testing procedures for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Single-step and step-wise methods are implemented. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models) are included. Results are reported in terms of adjusted p-values, confindence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. This Library is a part of the Bioconductor (bioconductor.org) proejct. -------------------------------------------------------------------------------- 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> 2.10.0-2 - rebuild for R 2.14.0 * Thu Nov 3 2011 pingou <pingou(a)pingoured.fr> 2.10.0-1 - Update to version 2.10.0 * Wed Jun 22 2011 pingou <pingou(a)pingoured.fr> 2.8.0-1 - Update to version 2.8.0 -------------------------------------------------------------------------------- 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-multtest' 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-RCurl-1.7.0-2.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-RCurl Product : Fedora 15 Version : 1.7.0 Release : 2.fc15 URL : http://cran.r-project.org/web/packages/RCurl/index.html Summary : General network (HTTP/FTP) client interface for R Description : The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc. -------------------------------------------------------------------------------- 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-RCurl' 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-Biobase-2.14.0-2.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-Biobase Product : Fedora 15 Version : 2.14.0 Release : 2.fc15 URL : http://bioconductor.org/packages/release/bioc/html/Biobase.html Summary : Base functions for Bioconductor Description : Base functions for Bioconductor (bioconductor.org). Biobase provides functions that are needed by many other Bioconductor packages or which replace R functions. -------------------------------------------------------------------------------- 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> 2.14.0-2 - rebuild for R 2.14.0 * Thu Nov 3 2011 pingou <pingou(a)pingoured.fr> 2.14.0-1 - Update to version 2.14.0 * Sun Jul 3 2011 pingou <pingou(a)pingoured.fr> 2.12.2-1 - Update to version 2.12.2 * Wed Jun 22 2011 pingou <pingou(a)pingoured.fr> 2.12.1-1 - Update to version 2.12.1 -------------------------------------------------------------------------------- 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-Biobase' 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-maanova-1.24.0-1.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-maanova Product : Fedora 15 Version : 1.24.0 Release : 1.fc15 URL : http://www.bioconductor.org/packages/release/bioc/html/maanova.html Summary : Analysis of N-dye Micro Array using mixed model effect Description : Analysis of N-dye Micro Array experiment using mixed model effect Containing analysis of variance, permutation and bootstrap, cluster and consensus tree -------------------------------------------------------------------------------- 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> 1.24.0-1 - update to 1.24.0 * Sat Jul 2 2011 pingou <pingou(a)pingoured.fr> 1.22.0-1 - Update to version 1.22.0 -------------------------------------------------------------------------------- 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-maanova' 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-ROC-1.30.0-1.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-ROC Product : Fedora 15 Version : 1.30.0 Release : 1.fc15 URL : http://bioconductor.org/packages/release/bioc/html/ROC.html Summary : Utilities for ROC Description : Utilities for ROC with uarray focus. -------------------------------------------------------------------------------- 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> 1.30.0-1 - update to 1.30.0 * Wed Jun 22 2011 pingou <pingou(a)pingoured.fr> 1.28.0-1 - Update to version 1.28.0 * Tue Mar 15 2011 pingou <pingou(a)pingoured.fr> 1.26.0-1 - Update to version 1.26.0 -------------------------------------------------------------------------------- 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-ROC' 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-hgu95av2probe-2.9.0-1.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-hgu95av2probe Product : Fedora 15 Version : 2.9.0 Release : 1.fc15 URL : http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2p… Summary : Probe sequence data for microarrays of type hgu95av2 Description : This package was automatically created by package matchprobes version 1.9.2. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95Av2\_probe\_tab. -------------------------------------------------------------------------------- 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> 2.9.0-1 - update to 2.9.0 * Sat Jul 2 2011 pingou <pingou(a)pingoured.fr> 2.8.0-1 - Update to version 2.8.0 -------------------------------------------------------------------------------- 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-hgu95av2probe' 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-hgu133acdf-2.9.1-1.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-hgu133acdf Product : Fedora 15 Version : 2.9.1 Release : 1.fc15 URL : http://www.bioconductor.org/packages/2.9/data/annotation/html/hgu133acdf.ht… Summary : HG-U133A.cdf data file Description : Environment representing the HG-U133A.cdf file. -------------------------------------------------------------------------------- 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> 2.9.1-1 - update to 2.9.1 * Wed Jun 22 2011 pingou <pingou(a)pingoured.fr> 2.8.0-1 - Update to version 2.8.0 * Tue Mar 15 2011 pingou <pingou(a)pingoured.fr> 2.7.0-1 - Update to version 2.7.0 -------------------------------------------------------------------------------- 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-hgu133acdf' 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-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-BSgenome.Celegans.UCSC.ce2 Product : Fedora 15 Version : 1.3.17 Release : 2.fc15 URL : http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.… Summary : Caenorhabditis elegans genome (UCSC Release ce2) Description : Caenorhabditis elegans genome grabbed from UCSC (ce2, Mar. 2004) and stored in Biostrings objects -------------------------------------------------------------------------------- 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> 1.3.17-2 - rebuild for R 2.14.0 * Sat Jul 2 2011 pingou <pingou(a)pingoured.fr> 1.3.17-1 - Update to version 1.3.17 -------------------------------------------------------------------------------- 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-BSgenome.Celegans.UCSC.ce2' 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-affydata-1.11.15-2.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-affydata Product : Fedora 15 Version : 1.11.15 Release : 2.fc15 URL : http://www.bioconductor.org/packages/2.6/data/experiment/html/affydata.html Summary : Affymetrix data for demonstration purpose Description : Example data sets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. -------------------------------------------------------------------------------- Update Information: Update R to 2.14.0. This required a mass rebuild of R components. -------------------------------------------------------------------------------- ChangeLog: * Tue Nov 8 2011 Tom Callaway <spot(a)fedoraproject.org> 1.11.15-2 - rebuild for R 2.14.0 * Thu Nov 3 2011 pingou <pingou(a)pingoured.fr> 1.11.15-1 - Update to version 1.11.15 * Tue Mar 15 2011 pingou <pingou(a)pingoured.fr> 1.11.11-1 - Update to version 1.11.11 -------------------------------------------------------------------------------- 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-affydata' 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-rtracklayer-1.14.1-2.fc15
by updates＠fedoraproject.org 28 Nov '11

28 Nov '11

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 -------------------------------------------------------------------------------- Name : R-rtracklayer Product : Fedora 15 Version : 1.14.1 Release : 2.fc15 URL : http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html Summary : R interface to genome browsers and their annotation tracks Description : Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport. -------------------------------------------------------------------------------- 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-rtracklayer' 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