[Bioc-devel] Bioconductor 3.5 release: db0, OrgDb and TxDb packages

[Obenchain, Valerie]

Hi,

The new db0, OrgDb and TxDb packages are now available in the devel branch.

# db0:

Updated all 19:

anopheles.db0_3.4.2.tar.gz
chicken.db0_3.4.2.tar.gz
fly.db0_3.4.2.tar.gz
pig.db0_3.4.2.tar.gz
xenopus.db0_3.4.2.tar.gz
arabidopsis.db0_3.4.2.tar.gz
chimp.db0_3.4.2.tar.gz
human.db0_3.4.2.tar.gz
rat.db0_3.4.2.tar.gz
yeast.db0_3.4.2.tar.gz
bovine.db0_3.4.2.tar.gz
ecoliK12.db0_3.4.2.tar.gz
malaria.db0_3.4.2.tar.gz
rhesus.db0_3.4.2.tar.gz
zebrafish.db0_3.4.2.tar.gz
canine.db0_3.4.2.tar.gz
ecoliSakai.db0_3.4.2.tar.gz
mouse.db0_3.4.2.tar.gz
worm.db0_3.4.2.tar.gz


# OrgDb:

Updated all 19:

org.Ce.eg.db_3.4.1.tar.gz
org.EcK12.eg.db_3.4.1.tar.gz
org.Mm.eg.db_3.4.1.tar.gz
org.Rn.eg.db_3.4.1.tar.gz
org.Ag.eg.db_3.4.1.tar.gz
org.Cf.eg.db_3.4.1.tar.gz
org.EcSakai.eg.db_3.4.1.tar.gz
org.Mmu.eg.db_3.4.1.tar.gz
org.Sc.sgd.db_3.4.1.tar.gz
org.At.tair.db_3.4.1.tar.gz
org.Dm.eg.db_3.4.1.tar.gz
org.Gg.eg.db_3.4.1.tar.gz
org.Pf.plasmo.db_3.4.1.tar.gz
org.Ss.eg.db_3.4.1.tar.gz
org.Bt.eg.db_3.4.1.tar.gz
org.Dr.eg.db_3.4.1.tar.gz
org.Hs.eg.db_3.4.1.tar.gz
org.Pt.eg.db_3.4.1.tar.gz
org.Xl.eg.db_3.4.1.tar.gz


# TxDb:

Added 1 new package:

TxDb.Ggallus.UCSC.galGal5.refGene_3.4.0.tar.gz

Updated 4 active tracks:

TxDb.Celegans.UCSC.ce11.refGene_3.4.1.tar.gz
TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.1.tar.gz
TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz 
TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.1.tar.gz


# Updated PFAM and GO:

PFAM.db_3.4.1.tar.gz
GO.db_3.4.1.tar.gz


I found what appear to be 2 abandoned OrgDb packages,
org.Tgondii.eg.db_1.0.tar.gz and org.Sco.eg.db_2.4.2.tar.gz. It looks
like these were last updated in October 2015. I've emailed the authors
but one bounced the other hasn't responded. Given that the OrgDb data
are a snapshot in time vs tied to a genome build it's important to
regenerate these every 6 months. If I don't hear back from the authors
I'll remove these from the repo.

Valerie


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