--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
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Name : R-RUnit
Product : Fedora 18
Version : 0.4.26
Release : 7.fc18
URL : http://cran.r-project.org/web/packages/RUnit/index.html
Summary : R Unit test framework
Description :
R functions implementing a standard Unit Testing framework, with additional
code inspection and report generation tools
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Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
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ChangeLog:
* Thu Apr 11 2013 Tom Callaway <spot(a)fedoraproject.org> - 0.4.26-7
- rebuild for R3
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 0.4.26-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
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This update can be installed with the "yum" update program. Use
su -c 'yum update R-RUnit' 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 Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
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Name : R-acepack
Product : Fedora 18
Version : 1.3.3.2
Release : 1.fc18
URL : http://cran.r-project.org/web/packages/acepack/index.html
Summary : ACE and AVAS methods for choosing regression transformations
Description :
ACE and AVAS (additivity and variance stabilization) are used to estimate
transformations for regression.
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Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
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ChangeLog:
* Thu Apr 11 2013 Tom Callaway <spot(a)fedoraproject.org> - 1.3.3.2-1
- update to 1.3.3.2
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.3.3.0-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use
su -c 'yum update R-acepack' 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
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Name : samtools
Product : Fedora 18
Version : 0.1.19
Release : 1.fc18
URL : http://samtools.sourceforge.net/
Summary : Tools for nucleotide sequence alignments in the SAM format
Description :
SAM (Sequence Alignment/Map) is a flexible generic format for storing
nucleotide sequence alignment.
SAM Tools provide various utilities for manipulating alignments in the
SAM format, including sorting, merging, indexing and generating
alignments in a per-position format.
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Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Thu Apr 11 2013 Tom Callaway <spot(a)fedoraproject.org> - 0.1.19-1
- update to 0.1.19
* Thu Feb 14 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 0.1.18-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use
su -c 'yum update samtools' 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
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Name : R-Rsolid
Product : Fedora 18
Version : 0.9.31
Release : 9.fc18
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.
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Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Fri Apr 12 2013 Tom Callaway <spot(a)fedoraproject.org> - 0.9.31-9
- rebuild for R3
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 0.9.31-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
--------------------------------------------------------------------------------
Name : R-XML
Product : Fedora 18
Version : 3.96.1.1
Release : 1.fc18
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".
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Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Thu Apr 4 2013 Pierre-Yves Chibon <pingou(a)pingoured.fr> 3.96.1.1-1
- Update to version 3.96.1.1
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 3.95.0.1-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Tue Nov 27 2012 pingou <pingou(a)pingoured.fr> 3.95.0.1-1
- Update to version 3.95.0.1
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
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Name : R-IRanges
Product : Fedora 18
Version : 1.18.0
Release : 2.fc18.1
URL : http://bioconductor.org/packages/release/bioc/html/IRanges.html
Summary : Low-level containers for storing sets of integer ranges
Description :
The IRanges class and its extensions are low-level containers
for storing sets of integer ranges. A typical use of these containers
in biology is for representing a set of chromosome regions.
More specific extensions of the IRanges class will typically
allow the storage of additional information attached to each
chromosome region as well as a hierarchical relationship between
these regions.
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Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Mon Apr 22 2013 Tom Callaway <spot(a)fedoraproject.org> - 1.18.0-2.1
- disable bootstrap
* Mon Apr 15 2013 Tom Callaway <spot(a)fedoraproject.org> - 1.18.0-2
- bootstrap pass
* Sun Apr 7 2013 pingou <pingou(a)pingoured.fr> 1.18.0-1
- Update to version 1.18.0
* Thu Feb 28 2013 pingou <pingou(a)pingoured.fr> 1.16.6-1
- Update to version 1.16.6
* Wed Feb 13 2013 pingou <pingou(a)pingoured.fr> 1.16.5-1
- Update to version 1.16.5
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.16.4-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Tue Nov 27 2012 pingou <pingou(a)pingoured.fr> 1.16.4-1
- Update to version 1.16.4
- + BR: R-GenomicRanges
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use
su -c 'yum update R-IRanges' 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
--------------------------------------------------------------------------------
Name : R-widgetTools
Product : Fedora 18
Version : 1.38.0
Release : 1.fc18
URL : http://bioconductor.org/packages/release/bioc/html/widgetTools.html
Summary : Bioconductor tools to support tcltk widgets
Description :
This package contains tools to support the construction of tcltk widgets.
This library is part of the bioconductor (bioconductor.org) project
--------------------------------------------------------------------------------
Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Sun Apr 7 2013 pingou <pingou(a)pingoured.fr> 1.38.0-1
- Update to version 1.38.0
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.36.0-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
* Tue Nov 27 2012 pingou <pingou(a)pingoured.fr> 1.36.0-1
- Update to version 1.36.0
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use
su -c 'yum update R-widgetTools' 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
--------------------------------------------------------------------------------
Name : R-zoo
Product : Fedora 18
Version : 1.7.9
Release : 1.fc18
URL : http://cran.r-project.org/web/packages/zoo/index.html
Summary : Z's ordered observations for irregular time series
Description :
An S3 class with methods for totally ordered indexed observations. It is
particularly aimed at irregular time series of numeric vectors/matrices and
factors. zoo's key design goals are independence of a particular index/date/
time class and consistency with with ts and base R by providing methods to
extend standard generics.
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Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Thu Apr 11 2013 Tom Callaway <spot(a)fedoraproject.org> - 1.7.9-1
- update to 1.7.9
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.7.6-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use
su -c 'yum update R-zoo' 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
--------------------------------------------------------------------------------
Name : R-abind
Product : Fedora 18
Version : 1.4.0
Release : 5.fc18
URL : http://cran.r-project.org/web/packages/abind/index.html
Summary : Combine multi-dimensional arrays
Description :
Combine multi-dimensional arrays. This is a generalization of cbind and rbind.
Takes a sequence of vectors, matrices, or arrays and produces a single array
of the same or higher dimension.
--------------------------------------------------------------------------------
Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Thu Apr 11 2013 Tom Callaway <spot(a)fedoraproject.org> - 1.4.0-5
- rebuild for R3
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.4.0-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use
su -c 'yum update R-abind' 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
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Fedora Update Notification
FEDORA-2013-6425
2013-04-24 00:40:11
--------------------------------------------------------------------------------
Name : R-bitops
Product : Fedora 18
Version : 1.0.5
Release : 1.fc18
URL : http://cran.r-project.org/web/packages/bitops/index.html
Summary : Functions for Bitwise operations
Description :
Functions for Bitwise operations on integer vectors.
--------------------------------------------------------------------------------
Update Information:
Update R to 3.0.0. This requires all R dependent packages (mostly R modules) to be rebuilt.
--------------------------------------------------------------------------------
ChangeLog:
* Thu Apr 11 2013 Tom Callaway <spot(a)fedoraproject.org> - 1.0.5-1
- update to 1.0.5
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng(a)lists.fedoraproject.org> - 1.0.4.1-9
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
--------------------------------------------------------------------------------
References:
[ 1 ] Bug #948083 - R-2.15.2-3 has a bug in kmeans
https://bugzilla.redhat.com/show_bug.cgi?id=948083
--------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use
su -c 'yum update R-bitops' 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
--------------------------------------------------------------------------------