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Fedora Update Notification
FEDORA-2018-050da4f07f
2018-05-31 14:34:44.120573
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Name : R-Rsolid
Product : Fedora 28
Version : 0.9.31
Release : 24.fc28
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 3.5.0. Rebuild rpy and rkward to match. rpy updated to 2.9.3 in
Fedora 28. All compiled R packages rebuilt (except for R-shogun, because shogun
doesn't build right now). Most updated to the latest version.
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ChangeLog:
* Fri May 18 2018 Tom Callaway <spot(a)fedoraproject.org> - 0.9.31-24
- rebuild for R 3.5.0
* Wed Feb 7 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 0.9.31-23
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
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References:
[ 1 ] Bug #1567573 - rpy-2.9.3 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1567573
[ 2 ] Bug #1570804 - R-3.5.0 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1570804
[ 3 ] Bug #1555530 - R-affyio: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555530
[ 4 ] Bug #1555528 - R-affy: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555528
[ 5 ] Bug #1555498 - R-Biostrings: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555498
[ 6 ] Bug #1555532 - R-bitops: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555532
[ 7 ] Bug #1555533 - R-caTools: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555533
[ 8 ] Bug #1560254 - R-curl-3.2 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1560254
[ 9 ] Bug #1575172 - R-httpuv-1.4.3 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1575172
[ 10 ] Bug #1563656 - R-lmtest-0.9-36 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1563656
[ 11 ] Bug #1555547 - R-maanova: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555547
[ 12 ] Bug #1555552 - R-msm: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555552
[ 13 ] Bug #1555555 - R-multtest: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555555
[ 14 ] Bug #1555556 - R-mvtnorm: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555556
[ 15 ] Bug #1555561 - R-preprocessCore: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555561
[ 16 ] Bug #1555564 - R-rlecuyer: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555564
[ 17 ] Bug #1555515 - R-ROC: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555515
[ 18 ] Bug #1555516 - R-RODBC: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555516
[ 19 ] Bug #1555521 - R-Rsolid: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555521
[ 20 ] Bug #1555569 - R-statmod: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555569
[ 21 ] Bug #1574116 - R-stringi-1.2.2 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1574116
[ 22 ] Bug #1555574 - R-waveslim: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555574
[ 23 ] Bug #1555575 - R-wavethresh: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555575
[ 24 ] Bug #1555525 - R-XML: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1555525
[ 25 ] Bug #1405667 - R-zoo-1.8-1 is available
https://bugzilla.redhat.com/show_bug.cgi?id=1405667
[ 26 ] Bug #1578961 - Review Request: R-prettyunits - Pretty, Human Readable Formatting
of Quantities
https://bugzilla.redhat.com/show_bug.cgi?id=1578961
[ 27 ] Bug #1578963 - Review Request: R-blob - A Simple S3 Class for Representing
Vectors of Binary Data ('BLOBS')
https://bugzilla.redhat.com/show_bug.cgi?id=1578963
[ 28 ] Bug #1556527 - v8-314: FTBFS in F28
https://bugzilla.redhat.com/show_bug.cgi?id=1556527
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This update can be installed with the "dnf" update program. Use
su -c 'dnf upgrade --advisory FEDORA-2018-050da4f07f' at the command
line. For more information, refer to the dnf documentation available at
http://dnf.readthedocs.io/en/latest/command_ref.html#upgrade-command-label
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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