[med-svn] [r-bioc-phyloseq] 03/06: Update upstream source from tag 'upstream/1.22.3'
Andreas Tille
tille at debian.org
Sat Nov 11 07:43:01 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-phyloseq.
commit 79805690c7651430a21b77b9746fdb7099695377
Merge: fb3d77c 47aabbd
Author: Andreas Tille <tille at debian.org>
Date: Sat Nov 11 08:33:18 2017 +0100
Update upstream source from tag 'upstream/1.22.3'
Update to upstream version '1.22.3'
with Debian dir 83a1800467d5c5db4c71fcf1fd321fce1943f63b
.travis.yml | 15 +++
DESCRIPTION | 28 ++---
NAMESPACE | 2 +
R/distance-methods.R | 7 +-
R/phylo-class.R | 9 --
R/plot-methods.R | 28 ++---
build/vignette.rds | Bin 347 -> 349 bytes
inst/doc/phyloseq-FAQ.R | 8 +-
inst/doc/phyloseq-FAQ.html | 147 ++++++++++++++++++----
inst/doc/phyloseq-analysis.R | 74 +++++------
inst/doc/phyloseq-analysis.html | 230 ++++++++++++++++++++++++----------
inst/doc/phyloseq-basics.R | 50 ++++----
inst/doc/phyloseq-basics.html | 127 ++++++++++++++++---
inst/doc/phyloseq-mixture-models.R | 24 ++--
inst/doc/phyloseq-mixture-models.html | 137 ++++++++++++++++----
man/DPCoA.Rd | 35 +++---
man/JSD.Rd | 9 +-
man/UniFrac-methods.Rd | 1 -
man/access.Rd | 1 -
man/assign-otu_table.Rd | 5 +-
man/assign-phy_tree.Rd | 3 +-
man/assign-sample_data.Rd | 3 +-
man/assign-sample_names.Rd | 5 +-
man/assign-tax_table.Rd | 7 +-
man/assign-taxa_are_rows.Rd | 3 +-
man/assign-taxa_names.Rd | 7 +-
man/build_tax_table.Rd | 1 -
man/capscale-phyloseq-methods.Rd | 3 +-
man/cca-rda-phyloseq-methods.Rd | 5 +-
man/chunkReOrder.Rd | 1 -
man/data-GlobalPatterns.Rd | 9 +-
man/data-enterotype.Rd | 7 +-
man/data-esophagus.Rd | 7 +-
man/data-soilrep.Rd | 7 +-
man/decorana.Rd | 1 -
man/dist-class.Rd | 1 -
man/distance.Rd | 3 +-
man/distanceMethodList.Rd | 1 -
man/envHash2otu_table.Rd | 1 -
man/estimate_richness.Rd | 1 -
man/export_env_file.Rd | 1 -
man/export_mothur_dist.Rd | 1 -
man/extract-methods.Rd | 3 +-
man/filter_taxa.Rd | 1 -
man/filterfun_sample.Rd | 1 -
man/fix_phylo.Rd | 1 -
man/gapstat_ord.Rd | 1 -
man/genefilter_sample-methods.Rd | 1 -
man/get.component.classes.Rd | 1 -
man/get_sample-methods.Rd | 1 -
man/get_taxa-methods.Rd | 1 -
man/get_taxa_unique.Rd | 1 -
man/get_variable.Rd | 1 -
man/getslots.phyloseq.Rd | 1 -
man/import.Rd | 1 -
man/import_RDP_cluster.Rd | 1 -
man/import_RDP_otu.Rd | 1 -
man/import_biom.Rd | 1 -
man/import_env_file.Rd | 1 -
man/import_mothur.Rd | 1 -
man/import_mothur_constaxonomy.Rd | 1 -
man/import_mothur_dist.Rd | 1 -
man/import_mothur_groups.Rd | 1 -
man/import_mothur_otu_table.Rd | 1 -
man/import_mothur_otulist.Rd | 1 -
man/import_mothur_shared.Rd | 1 -
man/import_pyrotagger_tab.Rd | 1 -
man/import_qiime.Rd | 1 -
man/import_qiime_otu_tax.Rd | 1 -
man/import_qiime_sample_data.Rd | 1 -
man/import_uparse.Rd | 1 -
man/import_usearch_uc.Rd | 1 -
man/index_reorder.Rd | 1 -
man/intersect_taxa.Rd | 1 -
man/make_network.Rd | 1 -
man/merge_phyloseq.Rd | 1 -
man/merge_phyloseq_pair-methods.Rd | 7 +-
man/merge_samples-methods.Rd | 3 +-
man/merge_taxa-methods.Rd | 7 +-
man/metaMDS.Rd | 1 -
man/microbio_me_qiime.Rd | 1 -
man/mt-methods.Rd | 9 +-
man/nodeplotblank.Rd | 1 -
man/nodeplotboot.Rd | 1 -
man/nodeplotdefault.Rd | 1 -
man/nsamples-methods.Rd | 3 +-
man/ntaxa-methods.Rd | 7 +-
man/ordinate.Rd | 1 -
man/otu_table-class.Rd | 1 -
man/otu_table-methods.Rd | 9 +-
man/parseTaxonomy-functions.Rd | 3 +-
man/pcoa.Rd | 1 -
man/phy_tree-methods.Rd | 1 -
man/phylo-class.Rd | 1 -
man/phylo.Rd | 1 -
man/phyloseq-class.Rd | 1 -
man/phyloseq-deprecated.Rd | 59 +++++----
man/phyloseq-package.Rd | 7 +-
man/phyloseq.Rd | 1 -
man/phyloseq_to_deseq2.Rd | 1 -
man/phyloseq_to_metagenomeSeq.Rd | 1 -
man/plot_bar.Rd | 1 -
man/plot_clusgap.Rd | 1 -
man/plot_heatmap.Rd | 1 -
man/plot_net.Rd | 1 -
man/plot_network.Rd | 1 -
man/plot_ordination.Rd | 1 -
man/plot_phyloseq-methods.Rd | 1 -
man/plot_richness.Rd | 1 -
man/plot_scree.Rd | 1 -
man/plot_tree.Rd | 1 -
man/prune_samples-methods.Rd | 3 +-
man/prune_taxa-methods.Rd | 9 +-
man/psmelt.Rd | 1 -
man/rank_names.Rd | 1 -
man/rarefy_even_depth.Rd | 1 -
man/read_tree.Rd | 1 -
man/read_tree_greengenes.Rd | 1 -
man/reconcile_categories.Rd | 1 -
man/refseq-methods.Rd | 1 -
man/rm_outlierf.Rd | 1 -
man/sample_data-class.Rd | 1 -
man/sample_data-methods.Rd | 1 -
man/sample_names-methods.Rd | 3 +-
man/sample_sums.Rd | 1 -
man/sample_variables.Rd | 1 -
man/show-methods.Rd | 3 +-
man/show_mothur_cutoffs.Rd | 1 -
man/splat.phyloseq.objects.Rd | 1 -
man/subset_ord_plot.Rd | 1 -
man/subset_samples-methods.Rd | 1 -
man/subset_taxa-methods.Rd | 1 -
man/tax_glom.Rd | 1 -
man/tax_table-methods.Rd | 3 +-
man/taxa_are_rows-methods.Rd | 1 -
man/taxa_names-methods.Rd | 9 +-
man/taxa_sums.Rd | 1 -
man/taxonomyTable-class.Rd | 1 -
man/threshrank.Rd | 1 -
man/threshrankfun.Rd | 1 -
man/tip_glom.Rd | 1 -
man/topf.Rd | 1 -
man/topk.Rd | 1 -
man/topp.Rd | 1 -
man/transformcounts.Rd | 4 +-
man/transpose-methods.Rd | 1 -
man/tree_layout.Rd | 1 -
tests/testthat/test-IO.R | 5 +-
148 files changed, 753 insertions(+), 505 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-phyloseq.git
More information about the debian-med-commit
mailing list