fixing more check problems

Author: zachary-foster

DESCRIPTION

@@ -54,7 +54,7 @@ Suggests:
     DESeq2
 VignetteBuilder: knitr
 RoxygenNote: 7.2.3
-Date: 2021-06-23
+Date: 2023-04-03
 Encoding: UTF-8
 biocViews: 
 LinkingTo: Rcpp

R/primersearch.R

@@ -105,7 +105,7 @@ parse_primersearch <- function(file_path) {
 #' 
 #' A pair of primers are aligned against a set of sequences.
 #' The location of the best hits, quality of match, and predicted amplicons are returned.
-#' Requires the EMBOSS tool kit (\url{http://emboss.sourceforge.net/}) to be installed.
+#' Requires the EMBOSS tool kit (\url{https://emboss.sourceforge.net/}) to be installed.
 #' 
 #' It can be confusing how the primer sequence relates to the binding sites on a
 #' reference database sequence. A simplified diagram can help. For example, if
@@ -347,7 +347,7 @@ primersearch_raw <- function(input = NULL, file = NULL, forward, reverse, mismat
 #' \code{\link{taxmap}} object with two tables is returned: a table with
 #' information for each predicted amplicon, quality of match, and predicted
 #' amplicons, and a table with per-taxon amplification statistics. Requires the
-#' EMBOSS tool kit (\url{http://emboss.sourceforge.net/}) to be installed.
+#' EMBOSS tool kit (\url{https://emboss.sourceforge.net/}) to be installed.
 #' 
 #' It can be confusing how the primer sequence relates to the binding sites on a
 #' reference database sequence. A simplified diagram can help. For example, if

README.Rmd

@@ -13,7 +13,6 @@ 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)](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)

README.md

@@ -1,9 +1,6 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-[![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)](https://www.r-pkg.org:443/pkg/metacoder)
 [![Downloads from Rstudio
@@ -24,17 +21,17 @@ color and size. It also provides various functions to do common tasks in
 microbiome bioinformatics on data in the `taxmap` format defined by the
 `taxa` package, such as:
 
--   Summing read counts/abundance per taxon
--   Converting counts to proportions and rarefaction of counts using
-    `vegan`
--   Comparing the abundance (or other characteristics) of groups of
-    samples (e.g., experimental treatments) per taxon
--   Combining data for groups of samples
--   Simulated PCR, via EMBOSS primersearch, for testing primer
-    specificity and coverage of taxonomic groups
--   Converting common microbiome formats for data and reference
-    databases into the objects defined by the `taxa` package.
--   Converting to and from the `phyloseq` format and the `taxa` format
+- Summing read counts/abundance per taxon
+- Converting counts to proportions and rarefaction of counts using
+  `vegan`
+- Comparing the abundance (or other characteristics) of groups of
+  samples (e.g., experimental treatments) per taxon
+- Combining data for groups of samples
+- Simulated PCR, via EMBOSS primersearch, for testing primer specificity
+  and coverage of taxonomic groups
+- Converting common microbiome formats for data and reference databases
+  into the objects defined by the `taxa` package.
+- Converting to and from the `phyloseq` format and the `taxa` format
 
 ## Installation
 
@@ -95,15 +92,15 @@ PLOS Computational Biology 13(2): e1005404.
 Metacoder is under active development and many new features are planned.
 Some improvements that are being explored include:
 
--   Barcoding gap analysis and associated plotting functions
--   A function to aid in retrieving appropriate sequence data from NCBI
-    for *in silico* PCR from whole genome sequences
--   Graphing of different node shapes in heat trees, possibly including
-    pie graphs or [PhyloPics](http://phylopic.org/).
--   Adding the ability to plot specific edge lengths in the heat trees
-    so they can be used for phylogenetic trees.
--   Adding more data import and export functions to make parsing and
-    writing common formats easier.
+- Barcoding gap analysis and associated plotting functions
+- A function to aid in retrieving appropriate sequence data from NCBI
+  for *in silico* PCR from whole genome sequences
+- Graphing of different node shapes in heat trees, possibly including
+  pie graphs or [PhyloPics](http://phylopic.org/).
+- Adding the ability to plot specific edge lengths in the heat trees so
+  they can be used for phylogenetic trees.
+- Adding more data import and export functions to make parsing and
+  writing common formats easier.
 
 To see the details of what is being worked on, check out the
 [issues](https://github.com/grunwaldlab/metacoder/issues) tab of the

cran-comments.md

@@ -1,25 +1,37 @@
 ## Test environments and check results
 
 
-### local: Pop!_OS 20.04 LTS, R 4.0.3 
+### local: Pop!_OS 22.04 LTS, R 4.2.2 
 
-0 errors | 0 warnings | 0 notes
+0 errors | 0 warnings | 1 notes
 
-### travis-ci: release
+❯ checking dependencies in R code ... NOTE
+  Namespace in Imports field not imported from: ‘R6’
+    All declared Imports should be used.
+    
+I am not sure why this note exists. I am using `R6::` in about 10 places in the package.
+All of the classes in the package are R6 classes, so it is definitely used. 
 
-0 errors | 0 warnings | 0 notes
 
-### Rhub: Ubuntu Linux 20.04.1 LTS, R-release, GCC
+### Rhub: Windows
 
-0 errors | 0 warnings | 0 notes
+0 errors | 0 warnings | 2 notes
 
-### All testing platforms using R devel (rhub, winbuilder)
+* checking dependencies in R code ... NOTE
+Namespace in Imports field not imported from: 'R6'
+  All declared Imports should be used.
+  
+I am not sure why this note exists. I am using `R6::` in about 10 places in the package.
+All of the classes in the package are R6 classes, so it is definitely used. 
 
-Some bioconductor packages in Suggests seem to not be available for R 4.2. I get the following error on R devel builds: 
+* checking for detritus in the temp directory ... NOTE
+Found the following files/directories:
+  'lastMiKTeXException'
 
-Error: Bioconductor does not yet build and check packages for R version 4.2
+Seems to be a bug with Rhub:
+
+https://github.com/r-hub/rhub/issues/503
 
-However, all of the bioconductor packages are optional and not needed for most functionality.
 
 
 ## Downstream dependencies