November 2011 - package-announce - Fedora Mailing-Lists

Fedora 16 Update: R-tkWidgets-1.32.0-2.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-tkWidgets Product : Fedora 16 Version : 1.32.0 Release : 2.fc16 URL : http://bioconductor.org/packages/release/bioc/html/tkWidgets.html Summary : Widgets to provide user interfaces from bioconductor Description : Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. This package is a part of the bioconductor (bioconductor.org) project -------------------------------------------------------------------------------- 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> 1.32.0-2 - rebuild for R 2.14.0 * Thu Nov 3 2011 pingou <pingou(a)pingoured.fr> 1.32.0-1 - Update to version 1.32.0 -------------------------------------------------------------------------------- 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-tkWidgets' 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: R-bigmemory-4.2.11-1.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-bigmemory Product : Fedora 16 Version : 4.2.11 Release : 1.fc16 URL : http://cran.r-project.org/web/packages/bigmemory/index.html Summary : Manage massive matrices in R using C++, with support for shared memory Description : Create, store, access, and manipulate massive matrices. Matrices are allocated to shared memory and may use memory-mapped files. Packages biganalytics, bigtabulate, synchronicity, and bigalgebra provide advanced functionality. -------------------------------------------------------------------------------- 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> - 4.2.11-1 - update to 4.2.11 -------------------------------------------------------------------------------- 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-bigmemory' 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: R-Biostrings-2.22.0-1.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-Biostrings Product : Fedora 16 Version : 2.22.0 Release : 1.fc16 URL : http://bioconductor.org/packages/release/bioc/html/Biostrings.html Summary : String objects representing biological sequences Description : Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences. -------------------------------------------------------------------------------- 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> 2.22.0-1 - update to 2.22.0 -------------------------------------------------------------------------------- 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-Biostrings' 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: R-XML-3.4.3-2.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-XML Product : Fedora 16 Version : 3.4.3 Release : 2.fc16 URL : http://cran.r-project.org/web/packages/XML/index.html Summary : Tools for parsing and generating xml within r and s-plus Description : This package provides many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. It also offers access to an XPath "interpreter". -------------------------------------------------------------------------------- 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> 3.4.3-2 - rebuild for R 2.14.0 * Thu Nov 3 2011 pingou <pingou(a)pingoured.fr> 3.4.3-1 - Update to version 3.4.3 -------------------------------------------------------------------------------- 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-XML' 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: R-msm-1.1-1.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-msm Product : Fedora 16 Version : 1.1 Release : 1.fc16 URL : http://cran.r-project.org/web/packages/msm/ Summary : Multi-state Markov and hidden Markov models in continuous time Description : Functions for fitting general continuous-time Markov and hidden Markov multi-state models to longitudinal data. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates. A variety of observation schemes are supported, including processes observed at arbitrary times, completely-observed processes, and censored states. -------------------------------------------------------------------------------- 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> - 1.1-1 - update to 1.1 -------------------------------------------------------------------------------- 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-msm' 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: R-RSQLite-0.10.0-1.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-RSQLite Product : Fedora 16 Version : 0.10.0 Release : 1.fc16 URL : http://cran.r-project.org/web/packages/RSQLite/index.html Summary : SQLite database interface for R Description : A SQLite database interface definition for communication between R and SQLite databases. -------------------------------------------------------------------------------- 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> - 0.10.0-1 - update to 0.10.0 -------------------------------------------------------------------------------- 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-RSQLite' 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: R-AnnotationDbi-1.16.0-2.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-AnnotationDbi Product : Fedora 16 Version : 1.16.0 Release : 2.fc16 URL : http://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html Summary : Annotation Database Interface Description : Provides user interface and database connection code for annotation data packages using SQLite data storage. -------------------------------------------------------------------------------- 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> 1.16.0-2 - rebuild for R 2.14.0 * Thu Nov 3 2011 pingou <pingou(a)pingoured.fr> 1.16.0-1 - Update to version 1.16.0 -------------------------------------------------------------------------------- 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-AnnotationDbi' 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: R-Rsolid-0.9.31-5.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-Rsolid Product : Fedora 16 Version : 0.9.31 Release : 5.fc16 URL : http://rafalab.jhsph.edu/Rsolid/ Summary : Quantile normalization and base calling for second generation sequencing data Description : Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample. Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls. The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance. -------------------------------------------------------------------------------- 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> - 0.9.31-5 - rebuild for R 2.14.0 -------------------------------------------------------------------------------- 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-Rsolid' 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: R-sciplot-1.0.9-1.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-sciplot Product : Fedora 16 Version : 1.0.9 Release : 1.fc16 URL : http://cran.r-project.org/web/packages/sciplot/index.html Summary : Scientific Graphing Functions for Factorial Designs Description : A collection of functions that creates graphs with error bars for data collected from one-way or higher factorial designs -------------------------------------------------------------------------------- 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> - 1.0.9-1 - update to 1.0-9 -------------------------------------------------------------------------------- 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-sciplot' 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: R-lmtest-0.9.29-1.fc16

by updates＠fedoraproject.org

-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15910 2011-11-15 23:36:23 -------------------------------------------------------------------------------- Name : R-lmtest Product : Fedora 16 Version : 0.9.29 Release : 1.fc16 URL : http://cran.r-project.org/web/packages/lmtest/index.html Summary : Testing Linear Regression Models for R Description : A collection of tests, data sets and examples for diagnostic checking in linear regression models in R. -------------------------------------------------------------------------------- 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> 0.9.29-1 - update to new R packaging model - update to 0.9-29 - rebuild against R 2.14.0 -------------------------------------------------------------------------------- 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-lmtest' 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