Binary files /tmp/tmp4EKy_Z/L7R23cEv80/r-bioc-biomformat-1.4.0/build/vignette.rds and /tmp/tmp4EKy_Z/2F_AQewLv4/r-bioc-biomformat-1.6.0/build/vignette.rds differ diff -Nru r-bioc-biomformat-1.4.0/debian/changelog r-bioc-biomformat-1.6.0/debian/changelog --- r-bioc-biomformat-1.4.0/debian/changelog 2017-09-30 08:39:37.000000000 +0000 +++ r-bioc-biomformat-1.6.0/debian/changelog 2017-11-10 07:51:18.000000000 +0000 @@ -1,3 +1,10 @@ +r-bioc-biomformat (1.6.0-1) unstable; urgency=medium + + * New upstream version + * Secure URI in watch file + + -- Andreas Tille Fri, 10 Nov 2017 08:51:18 +0100 + r-bioc-biomformat (1.4.0-1) unstable; urgency=medium * New upstream version diff -Nru r-bioc-biomformat-1.4.0/debian/watch r-bioc-biomformat-1.6.0/debian/watch --- r-bioc-biomformat-1.4.0/debian/watch 2017-09-30 08:39:37.000000000 +0000 +++ r-bioc-biomformat-1.6.0/debian/watch 2017-11-10 07:51:18.000000000 +0000 @@ -1,3 +1,3 @@ version=4 opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \ - http://www.bioconductor.org/packages/release/bioc/html/biomformat.html .*/biomformat_([\d\.]+)\.tar\.gz + https://www.bioconductor.org/packages/release/bioc/html/biomformat.html .*/biomformat_([\d\.]+)\.tar\.gz diff -Nru r-bioc-biomformat-1.4.0/DESCRIPTION r-bioc-biomformat-1.6.0/DESCRIPTION --- r-bioc-biomformat-1.4.0/DESCRIPTION 2017-04-25 00:27:37.000000000 +0000 +++ r-bioc-biomformat-1.6.0/DESCRIPTION 2017-10-31 00:35:43.000000000 +0000 @@ -1,5 +1,5 @@ Package: biomformat -Version: 1.4.0 +Version: 1.6.0 Date: 2016-04-16 Maintainer: Paul J. McMurdie License: GPL-2 @@ -22,4 +22,4 @@ 'validity-methods.R' biocViews: DataImport, Metagenomics, Microbiome NeedsCompilation: no -Packaged: 2017-04-25 00:27:37 UTC; biocbuild +Packaged: 2017-10-31 00:35:43 UTC; biocbuild diff -Nru r-bioc-biomformat-1.4.0/inst/doc/biomformat.html r-bioc-biomformat-1.6.0/inst/doc/biomformat.html --- r-bioc-biomformat-1.4.0/inst/doc/biomformat.html 2017-04-25 00:27:36.000000000 +0000 +++ r-bioc-biomformat-1.6.0/inst/doc/biomformat.html 2017-10-31 00:35:43.000000000 +0000 @@ -4,23 +4,30 @@ - + + + The biomformat package vignette + + + + + + + - - + + + + + + + +

+ + + + + + + + + + + +

+ + + +

The biomformat package vignette

Paul J. McMurdie

30 October 2017

@@ -78,9 +145,9 @@

This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages. Further details on R markdown here.

The BIOM file format (canonically pronounced “biome”) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project. Please see the biom-format home page for more details.

This demo is designed to provide an overview of the biom package to get you started using it quickly. The biom package itself is intended to be a utility package that will be depended-upon by other packages in the future. It provides I/O functionality, and functions to make it easier to with data from biom-format files. It does not (and probably should not) provide statistical analysis functions. However, it does provide tools to access data from BIOM format files in ways that are extremely common in R (such as "data.frame", "matrix", and "Matrix" classes).

Package versions at the time (Mon Apr 24 20:27:33 2017) of this build:

Package versions at the time (Mon Oct 30 20:35:37 2017) of this build:

library("biomformat"); packageVersion("biomformat")

## [1] '1.4.0'

## [1] '1.6.0'

1 Read BIOM format

@@ -199,11 +266,11 @@

2.0.4 Plots

The data really is accessible to other R functions.

plot(biom_data(x4))

boxplot(as(biom_data(x4), "vector"))

heatmap(as(biom_data(x4), "matrix"))

@@ -223,12 +290,41 @@ + +

+ + + + diff -Nru r-bioc-biomformat-1.4.0/inst/doc/biomformat.R r-bioc-biomformat-1.6.0/inst/doc/biomformat.R --- r-bioc-biomformat-1.4.0/inst/doc/biomformat.R 2017-04-25 00:27:36.000000000 +0000 +++ r-bioc-biomformat-1.6.0/inst/doc/biomformat.R 2017-10-31 00:35:42.000000000 +0000 @@ -1,7 +1,7 @@ -## ----packages------------------------------------------------------------ +## ----packages-------------------------------------------------------------- library("biomformat"); packageVersion("biomformat") -## ----read-biom-examples-------------------------------------------------- +## ----read-biom-examples---------------------------------------------------- min_dense_file = system.file("extdata", "min_dense_otu_table.biom", package = "biomformat") min_sparse_file = system.file("extdata", "min_sparse_otu_table.biom", @@ -21,39 +21,39 @@ x6 = read_biom(rich_sparse_char) x1 -## ----accessor-examples-table--------------------------------------------- +## ----accessor-examples-table----------------------------------------------- biom_data(x1) biom_data(x2) -## ----matrix-coercion----------------------------------------------------- +## ----matrix-coercion------------------------------------------------------- as(biom_data(x2), "matrix") -## ----observ-meta--------------------------------------------------------- +## ----observ-meta----------------------------------------------------------- observation_metadata(x1) observation_metadata(x2) observation_metadata(x3) observation_metadata(x4)[1:2, 1:3] class(observation_metadata(x4)) -## ----plot-examples------------------------------------------------------- +## ----plot-examples--------------------------------------------------------- sample_metadata(x1) sample_metadata(x2) sample_metadata(x3) sample_metadata(x4)[1:2, 1:3] class(sample_metadata(x4)) -## ----plot---------------------------------------------------------------- +## ----plot------------------------------------------------------------------ plot(biom_data(x4)) boxplot(as(biom_data(x4), "vector")) heatmap(as(biom_data(x4), "matrix")) -## ----write-biom-examples------------------------------------------------- +## ----write-biom-examples--------------------------------------------------- outfile = tempfile() write_biom(x4, outfile) y = read_biom(outfile) identical(x4, y) -## ----compare-files-diff, eval=FALSE-------------------------------------- +## ----compare-files-diff, eval=FALSE---------------------------------------- # # On Unix OSes # system(paste0("diff ", rich_sparse_file, outfile)) # # On windows

The biomformat package vignette

30 October 2017

The biomformat package vignette

Paul J. McMurdie

Contents

1 Read BIOM format

2.0.4 Plots