preparing for CRAN submission

Author: zachary-foster

DESCRIPTION

@@ -53,7 +53,7 @@ Suggests:
     biomformat
 VignetteBuilder: knitr
 RoxygenNote: 7.1.1
-Date: 2020-04-28
+Date: 2021-06-23
 Encoding: UTF-8
 biocViews: 
 LinkingTo: Rcpp

NEWS.md

@@ -1,10 +1,12 @@
 # News 
 
-## Current 
+## metacoder 0.3.5 
 
 * Replaced depreciated `as.tbl` function from `dplyr`'
 * Added `node_legend_title` and `edge_legend_title` options to `heat_tree` to specify the title for each legend.
 * Added options to `heat_tree` to set the number of significant fingures used for the numbers in the legend.
+* Reintegrated the functionality of the `taxa` package in order to prepare for releasing a rewritten version of taxa.
+* Reduced the number of dependencies and made some optional. 
 
 ##  metacoder 0.3.4
 
@@ -102,8 +104,8 @@
 * Added functions to identift and remove taxa with ambiguous names like "unknown"
 * code from [ggrepel](https://github.com/slowkow/ggrepel) package now used to avoid overlapping labels. Thanks Kamil Slowikowski!
 * New function `heat_tree_matrix` to make plotting a pairwise matrix of heat trees for comparing treatments.
-* New parser named `parse_mothur_tax_summary` for mothur *.tax.summary file made by [classify.seqs](https://www.mothur.org/wiki/Classify.seqs).
-* New parser named `parse_mothur_taxonomy` for mothur *.taxonomy file made by [classify.seqs](https://www.mothur.org/wiki/Classify.seqs).
+* New parser named `parse_mothur_tax_summary` for mothur *.tax.summary file made by [classify.seqs](https://mothur.org/wiki/Classify.seqs).
+* New parser named `parse_mothur_taxonomy` for mothur *.taxonomy file made by [classify.seqs](https://mothur.org/wiki/Classify.seqs).
 * New parser named `parse_qiime_biom` for the QIIME BIOM output.
 * New parser named `parse_phyloseq` to convert phyloseq objects.
 * New parser named `parse_newick` to parse newick files.

R/metacoder-package.R

@@ -17,7 +17,7 @@
 #' 
 #' @section Documentation:
 #' 
-#' The full documentation can be found online at \url{http://grunwaldlab.github.io/metacoder_documentation}.
+#' The full documentation can be found online at \url{https://grunwaldlab.github.io/metacoder_documentation/}.
 #' 
 #' There is also a short vignette included for offline use that can be accessed  by the following code:
 #' 

R/primersearch.R

@@ -179,7 +179,7 @@ parse_primersearch <- function(file_path) {
 #' 
 #' \strong{Mac OSX:}
 #' 
-#' The easiest way to install EMBOSS on OSX is to use \href{http://brew.sh/}{homebrew}.
+#' The easiest way to install EMBOSS on OSX is to use \href{https://brew.sh/}{homebrew}.
 #' After installing homebrew, open up a terminal and type:
 #' 
 #' \code{brew install homebrew/science/emboss}
@@ -458,7 +458,7 @@ primersearch_raw <- function(input = NULL, file = NULL, forward, reverse, mismat
 #' 
 #' \strong{Mac OSX:}
 #' 
-#' The easiest way to install EMBOSS on OSX is to use \href{http://brew.sh/}{homebrew}.
+#' The easiest way to install EMBOSS on OSX is to use \href{https://brew.sh/}{homebrew}.
 #' After installing homebrew, open up a terminal and type:
 #' 
 #' \code{brew install homebrew/science/emboss}

README.Rmd

@@ -14,8 +14,8 @@ knitr::opts_chunk$set(
 
 
 [![Build Status](https://travis-ci.com/grunwaldlab/metacoder.png?branch=master)](https://travis-ci.com/grunwaldlab/metacoder?branch=master) [![codecov.io](https://codecov.io/github/grunwaldlab/metacoder/coverage.svg?branch=master)](https://codecov.io/github/grunwaldlab/metacoder?branch=master)
-[![Downloads from Rstudio mirror per month](http://cranlogs.r-pkg.org/badges/metacoder)](http://www.r-pkg.org/pkg/metacoder)
-[![Downloads from Rstudio mirror](http://cranlogs.r-pkg.org/badges/grand-total/metacoder)](http://www.r-pkg.org/pkg/metacoder)
+[![Downloads from Rstudio mirror per month](http://cranlogs.r-pkg.org/badges/metacoder)](https://www.r-pkg.org:443/pkg/metacoder)
+[![Downloads from Rstudio mirror](http://cranlogs.r-pkg.org/badges/grand-total/metacoder)](https://www.r-pkg.org:443/pkg/metacoder)
 [![CRAN version](http://www.r-pkg.org/badges/version/metacoder)](https://cran.r-project.org/package=metacoder)
 
 ![](man/figures/readme_figure.jpg)
@@ -78,7 +78,7 @@ You can also combine the two in a single analysis by converting between the two
 
 ## Citation
 
-If you use metcoder in a publication, please cite our [article in PLOS Computational Biology](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404):
+If you use metcoder in a publication, please cite our [article in PLOS Computational Biology](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404):
 
 Foster ZSL, Sharpton TJ, Grünwald NJ (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLOS Computational Biology 13(2): e1005404. https://doi.org/10.1371/journal.pcbi.1005404
 

cran-comments.md

@@ -1,36 +1,32 @@
 ## Test environments and check results
 
-Some packages seem to not be avaialble for R 4.0.0. I am not sure what to do about this. It works on my computer and winbuilder.
 
-### local: ubuntu 18.04, R 3.6.3
+### local: Pop!_OS 20.04 LTS, R 4.0.3 
 
 0 errors | 0 warnings | 0 notes
 
-### travis-ci: ubuntu 14.04.05, R development
+### travis-ci: release
+
+0 errors | 0 warnings | 0 notes
+
+
+### Rhub: Windows Server 2008 R2 SP1, R-devel, 32/64 bit
+
+Some bioconductor packages in Suggests seem to not be available for R 4.2. I get the following error on R devel builds: 
+
+Error: Bioconductor does not yet build and check packages for R version 4.2
+
+However, all of the bioconductor pacakges are optional and not needed for most functionality.
 
-Warning message:
 
-package ‘BiocManager, zlibbioc’ is not available (for R Under development) 
 
-The command "Rscript -e 'install.packages(c("BiocManager, zlibbioc"));if (!all(c("BiocManager, zlibbioc") %in% installed.packages())) { q(status = 1, save = "no")}'" failed and exited with 1 during .
 
-### travis-ci: ubuntu 14.04.05, bioc-release
 
-Warning message:
 
-package ‘BiocManager, zlibbioc’ is not available (for R version 4.0.0) 
 
-The command "Rscript -e 'install.packages(c("BiocManager, zlibbioc"));if (!all(c("BiocManager, zlibbioc") %in% installed.packages())) { q(status = 1, save = "no")}'" failed and exited with 1 during .
 
 
-### Rhub: Windows Server 2008 R2 SP1, R-devel, 32/64 bit
 
-* checking package dependencies ... ERROR
-Packages required but not available:
-  'taxa', 'stringr', 'ggplot2', 'igraph', 'scales', 'taxize', 'seqinr',
-  'reshape2', 'zoo', 'traits', 'RCurl', 'ape', 'reshape', 'lazyeval',
-  'dplyr', 'readr', 'rlang', 'biomformat', 'ggfittext', 'vegan',
-  'ggrepel', 'cowplot', 'GA', 'Rcpp', 'svglite', 'tibble'
 
 ### Win builder: R devel
 

inst/CITATION

@@ -11,4 +11,4 @@ bibentry(bibtype = "Article",
          pages = "1-15",
          number = "2",
          doi = "10.1371/journal.pcbi.1005404",
-         url = "http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404")
+         url = "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404")