Fedora 19 Update: R-qtl-1.32.10-3.fc19

Thu Jul 10 00:25:31 UTC 2014

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Fedora Update Notification
FEDORA-2014-7986
2014-07-01 22:36:13
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Name        : R-qtl
Product     : Fedora 19
Version     : 1.32.10
Release     : 3.fc19
URL         : http://www.rqtl.org/
Summary     : Tools for analyzing QTL experiments
Description :
R-qtl is an extensible, interactive environment for mapping
quantitative trait loci (QTLs) in experimental crosses. Our goal is to
make complex QTL mapping methods widely accessible and allow users to
focus on modeling rather than computing.

A key component of computational methods for QTL mapping is the hidden
Markov model (HMM) technology for dealing with missing genotype
data. We have implemented the main HMM algorithms, with allowance for
the presence of genotyping errors, for backcrosses, intercrosses, and
phase-known four-way crosses.

The current version of R-qtl includes facilities for estimating
genetic maps, identifying genotyping errors, and performing single-QTL
genome scans and two-QTL, two-dimensional genome scans, by interval
mapping (with the EM algorithm), Haley-Knott regression, and multiple
imputation. All of this may be done in the presence of covariates
(such as sex, age or treatment). One may also fit higher-order QTL
models by multiple imputation and Haley-Knott regression.

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Update Information:

- run tests also on secondary arches
Version 1.32, 2014-05-28:

Major changes:

* None.

Minor changes:

* fitqtl with model="normal" now returns residuals as an attribute.
* Added an additional argument to plot.scanone, bgrect, for making the background of the plotting region a different color.
* Revised cleanGeno to work with any cross having two possible genotypes (i.e., not just bc but also riself, risib, dh, haploid).
* Revised summary.cross so that overall genotype frequencies are given separately for autosomes and the X chromosome.
* Fixed typo in a warning in add.threshold.
* Fixed a bug in reduce2grid, regarding format of attributes
* Fixed a bug in MQM: in some circumstances, the last marker was always included as cofactor; other cleanup in MQM code.

Version 1.32, 2014-05-28:

Major changes:

* None.

Minor changes:

* fitqtl with model="normal" now returns residuals as an attribute.
* Added an additional argument to plot.scanone, bgrect, for making the background of the plotting region a different color.
* Revised cleanGeno to work with any cross having two possible genotypes (i.e., not just bc but also riself, risib, dh, haploid).
* Revised summary.cross so that overall genotype frequencies are given separately for autosomes and the X chromosome.
* Fixed typo in a warning in add.threshold.
* Fixed a bug in reduce2grid, regarding format of attributes
* Fixed a bug in MQM: in some circumstances, the last marker was always included as cofactor; other cleanup in MQM code.

Version 1.32, 2014-05-28:

Major changes:

* None.

Minor changes:

* fitqtl with model="normal" now returns residuals as an attribute.
* Added an additional argument to plot.scanone, bgrect, for making the background of the plotting region a different color.
* Revised cleanGeno to work with any cross having two possible genotypes (i.e., not just bc but also riself, risib, dh, haploid).
* Revised summary.cross so that overall genotype frequencies are given separately for autosomes and the X chromosome.
* Fixed typo in a warning in add.threshold.
* Fixed a bug in reduce2grid, regarding format of attributes
* Fixed a bug in MQM: in some circumstances, the last marker was always included as cofactor; other cleanup in MQM code.

Version 1.32, 2014-05-28:

Major changes:

* None.

Minor changes:

* fitqtl with model="normal" now returns residuals as an attribute.
* Added an additional argument to plot.scanone, bgrect, for making the background of the plotting region a different color.
* Revised cleanGeno to work with any cross having two possible genotypes (i.e., not just bc but also riself, risib, dh, haploid).
* Revised summary.cross so that overall genotype frequencies are given separately for autosomes and the X chromosome.
* Fixed typo in a warning in add.threshold.
* Fixed a bug in reduce2grid, regarding format of attributes
* Fixed a bug in MQM: in some circumstances, the last marker was always included as cofactor; other cleanup in MQM code.

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ChangeLog:

* Tue Jul  1 2014 Jakub Čajka <jcajka at redhat.com> - 1.32.10-3
- Changed stack limit on ppc64 and s390x to allow checks to pass
* Sat Jun 28 2014 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.32.10-2
- Disable checks on ppc64
* Wed Jun 25 2014 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.32.10-1
- Update to 1.32.10
- Use R-core-devel instead of R-devel as BR
- Re-enable checks
* Fri Jun  6 2014 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.31.9-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Thu May  8 2014 Tom Callaway <spot at fedoraproject.org> - 1.31.9-1
- Update to 1.31.9
* Sat Dec 21 2013 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.29.2-1
- Update to 1.29.2
- Add BR for blas-devel and lapack-devel
* Tue Oct 15 2013 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.28.19-1
- Update to 1.28.19
* Fri Aug  2 2013 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.27.10-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
* Wed Apr 17 2013 Tom Callaway <spot at fedoraproject.org> - 1.27.10-2
- rebuild for R3
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This update can be installed with the "yum" update program.  Use
su -c 'yum update R-qtl' 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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