[med-svn] [r-bioc-phyloseq] branch master updated (812ec5a -> de31569)
Andreas Tille
tille at debian.org
Sat Nov 11 07:43:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-bioc-phyloseq.
from 812ec5a Standards-Version: 4.1.1
new fb3d77c Secure URI in watch file
new 47aabbd New upstream version 1.22.3
new 7980569 Update upstream source from tag 'upstream/1.22.3'
new f796d00 New upstream version
new 04f20c4 Adapt patch
new de31569 Upload to unstable
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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
debian/changelog | 7 +
debian/patches/fix_r-cran-ade4_versioning.patch | 10 +-
debian/watch | 2 +-
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 +-
151 files changed, 766 insertions(+), 511 deletions(-)
create mode 100644 .travis.yml
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