Merge pull request #81 from adrientaudiere/dev

Improve test and examples for CRAN submission - mainly for windows build
adrientaudiere · Feb 10, 2024 · e862ec5 · e862ec5
2 parents 14da7e5 + b7f917f
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diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -34,6 +34,9 @@ jobs:
       - name: Install blastn
         run: sudo apt-get install ncbi-blast+
 
+      - name: Install R packages not in DESCRIPTION
+        run: Rscript -e 'pak::pkg_install(c(datawizard, formattable, ggforce, ggtree, gtExtras, MicrobiotaProcess, pillar, pointblank, summarytools, svglite, tidytree, treeio))'
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, clean = TRUE)
         shell: Rscript {0}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MiscMetabar
 Type: Package
 Title: Miscellaneous Functions for Metabarcoding Analysis
-Version: 0.7.4
+Version: 0.7.5
 Authors@R: person("Adrien", "Taudière", email = "[email protected]",
   role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-1088-1182"))
 Description: The MiscMetabar package aims to facilitate the description, transformation, exploration, and reproducibility of metabarcoding analysis. Mainly build on the top of phyloseq, dada2 R packages. MiscMetabar help to build reproducible and robust bioinformatic pipeline in R. MiscMetabar make ecological analysis of alpha and beta-diversity simple and powerful by integrating a large number of analysis, some of them from other R packages.  
@@ -74,19 +74,7 @@ Suggests:
     venneuler,
     vctrs,
     viridis,
-    withr,
-    datawizard,
-    formattable,
-    ggforce,
-    ggtree,
-    gtExtras,
-    MicrobiotaProcess,
-    pillar,
-    pointblank,
-    summarytools,   
-    svglite,
-    tidytree,
-    treeio
+    withr
 RoxygenNote: 7.3.1
 URL: https://github.com/adrientaudiere/MiscMetabar,
     https://adrientaudiere.github.io/MiscMetabar/

diff --git a/R/Deseq2_edgeR.R b/R/Deseq2_edgeR.R
@@ -19,7 +19,7 @@
 #'   or \code{\link[ggplot2]{ggplot}}
 #'
 #' @export
-#' @examples
+#' @examplesIf  tolower(Sys.info()[["sysname"]]) != "windows"
 #' data("GlobalPatterns", package = "phyloseq")
 #' GP_archae <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
 #' plot_edgeR_pq(GP_archae, c("SampleType", "Soil", "Feces"),

diff --git a/R/dada_phyloseq.R b/R/dada_phyloseq.R
@@ -227,6 +227,10 @@ clean_pq <- function(physeq,
 #' @return The number of sequences, clusters (e.g. OTUs, ASVs) and samples for
 #'   each object.
 #' @export
+#' @seealso [track_wkflow_samples()]
+#' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
+#' data(enterotype)
+#' track_wkflow(list(data_fungi, enterotype), taxonomy_rank = c(3, 5))
 
 track_wkflow <- function(list_of_objects,
                          obj_names = NULL,
@@ -436,8 +440,7 @@ track_wkflow <- function(list_of_objects,
 #' @export
 #' @author Adrien Taudière
 #'
-#' @examples
-#'
+#' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
 #' tree_A10_005 <- subset_samples(data_fungi, Tree_name == "A10-005")
 #' track_wkflow_samples(tree_A10_005)
 track_wkflow_samples <- function(list_pq_obj, ...) {

diff --git a/R/krona.R b/R/krona.R
@@ -19,11 +19,14 @@
 #'   your krona result files before merging using [merge_krona()]
 #'
 #' @examples
+#' 
 #' data("GlobalPatterns", package = "phyloseq")
 #' GA <- subset_taxa(GlobalPatterns, Phylum == "Acidobacteria")
-#' # krona(GA, "Number.of.sequences.html")
-#' # krona(GA, "Number.of.ASVs.html", nb_seq = FALSE)
-#' # merge_krona(c("Number.of.sequences.html", "Number.of.ASVs.html"))
+#' \dontrun{
+#'  krona(GA, "Number.of.sequences.html")
+#'  krona(GA, "Number.of.ASVs.html", nb_seq = FALSE)
+#'  merge_krona(c("Number.of.sequences.html", "Number.of.ASVs.html"))
+#' }
 #' @return A html file
 #' @export
 #' @seealso \code{\link{merge_krona}}
@@ -107,8 +110,7 @@ krona <-
 #' @param output path to the output file
 #'
 #' @examples
-#' krona_error_or_not <- try(system("ktImportText 2>&1", intern = TRUE))
-#' if (class(krona_error_or_not) != "try-error") {
+#' \dontrun{
 #'   data("GlobalPatterns", package = "phyloseq")
 #'   GA <- subset_taxa(GlobalPatterns, Phylum == "Acidobacteria")
 #'   krona(GA, "Number.of.sequences.html", name = "Nb_seq_GP_acidobacteria")

diff --git a/R/miscellanous.R b/R/miscellanous.R
@@ -195,7 +195,7 @@ perc <- function(x, y = NULL, accuracy = 0, add_symbol = FALSE) {
 #' @return the number of sequences
 #' @author Adrien Taudière
 #' @export
-#' @examples
+#' @examplesIf tolower(Sys.info()[["sysname"]]) != "windows"
 #' count_seq(file_path = system.file(
 #'   "extdata",
 #'   "ex.fasta",

diff --git a/README.Rmd b/README.Rmd
@@ -76,7 +76,6 @@ The article [filter taxa and samples](https://adrientaudiere.github.io/MiscMetab
 
 For developers, I also wrote a article describing som [rules of codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html). 
 
-
 ### Summarize a physeq object
 
 ```{r example}
@@ -109,11 +108,17 @@ ggvenn_pq(data_fungi, fact = "Height") +
   labs(title = "Share number of ASV among Height in tree")
 ```
 
+### Note for non-linux users
+
+Some functions may not work on windows (*e.g.* [track_wflow()], [cutadapt_remove_primers()], [krona()], [vsearch_clustering()], ...). A solution is to exploit docker container, for example the using the great [rocker project](https://rocker-project.org/).
+
+MiscMetabar is developed under Linux and the vast majority of functions may works on Unix system, but its functionning is not test under iOS.
+
 ### Installation of other softwares for debian Linux distributions
 
 If you encounter any errors or have any questions about the installation of these softwares, please visit their dedicated websites. 
 
-#### [blast@](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata)
+#### [blast+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata)
 
 ```sh
 sudo apt-get install ncbi-blast+

diff --git a/README.md b/README.md
@@ -155,12 +155,22 @@ ggvenn_pq(data_fungi, fact = "Height") +
 
 <img src="man/figures/README-unnamed-chunk-6-1.png" width="100%" />
 
+### Note for non-linux users
+
+Some functions may not work on windows (*e.g.* \[track_wflow()\],
+\[cutadapt_remove_primers()\], \[krona()\], \[vsearch_clustering()\],
+…). A solution is to exploit docker container, for example the using the
+great [rocker project](https://rocker-project.org/).
+
+MiscMetabar is developed under Linux and the vast majority of functions
+may works on Unix system, but its functionning is not test under iOS.
+
 ### Installation of other softwares for debian Linux distributions
 
 If you encounter any errors or have any questions about the installation
 of these softwares, please visit their dedicated websites.
 
-#### [blast@](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata)
+#### [blast+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata)
 
 ``` sh
 sudo apt-get install ncbi-blast+

diff --git a/man/count_seq.Rd b/man/count_seq.Rd
diff --git a/man/krona.Rd b/man/krona.Rd
diff --git a/man/merge_krona.Rd b/man/merge_krona.Rd
diff --git a/man/plot_edgeR_pq.Rd b/man/plot_edgeR_pq.Rd
diff --git a/man/track_wkflow.Rd b/man/track_wkflow.Rd
diff --git a/man/track_wkflow_samples.Rd b/man/track_wkflow_samples.Rd
diff --git a/tests/testthat/test_cutadapt.R b/tests/testthat/test_cutadapt.R
@@ -5,6 +5,8 @@ if (!MiscMetabar:::is_cutadapt_installed()) {
   )
 } else {
   test_that("cutadapt_remove_primers works fine", {
+    skip_on_cran()
+    skip_on_os("windows")
     expect_silent(suppressMessages(
       res_cut <- cutadapt_remove_primers("inst/extdata", "TTC", "GAA",
         folder_output = paste0(tempdir(), "/output_cutadapt")

diff --git a/tests/testthat/test_figures_beta_div.R b/tests/testthat/test_figures_beta_div.R
@@ -368,6 +368,7 @@ test_that("plot_SCBD_pq works with data_fungi_mini dataset", {
 })
 
 test_that("multipatt_pq works with data_fungi_mini dataset", {
+  skip_on_os("windows")
   expect_s3_class(
     multipatt_pq(subset_samples(data_fungi_mini, !is.na(Time)),
       fact = "Time"
@@ -378,6 +379,7 @@ test_that("multipatt_pq works with data_fungi_mini dataset", {
 })
 
 test_that("multipatt_pq works with data_fungi_mini dataset", {
+  skip_on_os("windows")
   expect_type(suppressMessages(suppressWarnings(res_height <- ancombc_pq(
     subset_taxa_pq(
       data_fungi_sp_known,

diff --git a/tests/testthat/test_figures_taxo.R b/tests/testthat/test_figures_taxo.R
@@ -13,6 +13,7 @@ GP_archae <-
   subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
 
 test_that("rotl_pq works with data_fungi dataset", {
+  skip_on_os("windows")
   library("rotl")
   expect_s3_class(suppressWarnings(tr <-
     rotl_pq(data_fungi, species_colnames = "Genus_species")), "phylo")
@@ -385,7 +386,7 @@ test_that("add_funguild_info and plot_guild_pq work with data_fungi_mini dataset
 
 
 test_that("build_phytree_pq work with data_fungi dataset", {
-  library("phangorn")
+  skip_on_os("windows")
   df <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 19000)
   expect_type(df_tree <- build_phytree_pq(df, nb_bootstrap = 2, rearrangement = "stochastic"), "list")
   expect_type(df_tree <- build_phytree_pq(df, nb_bootstrap = 2, rearrangement = "ratchet"), "list")

diff --git a/tests/testthat/test_krona.R b/tests/testthat/test_krona.R
@@ -4,6 +4,8 @@ GA <- subset_taxa(GlobalPatterns, Phylum == "Acidobacteria")
 krona_error_or_not <- try(system("ktImportText 2>&1", intern = TRUE))
 
 if (class(krona_error_or_not) == "try-error") {
+  skip_on_cran()
+  skip_on_os("windows")
   test_that("krona send an error when krona is not installed", {
     expect_warning(krona(GA, "Number.of.sequences.html"))
     expect_warning(krona(GA, "Number.of.ASVs.html", nb_seq = FALSE))

diff --git a/tests/testthat/test_phyloseq_class.R b/tests/testthat/test_phyloseq_class.R
@@ -90,6 +90,7 @@ test_that("perc works fine", {
 })
 
 test_that("count_seq works fine", {
+  skip_on_os("windows")
   expect_equal(count_seq("inst/extdata/ex_R1_001.fastq.gz"), 2500)
   expect_equal(count_seq("inst/extdata/ex_R2_001.fastq.gz"), 2500)
   expect_equal(count_seq("inst/extdata/ex.fasta"), 3)

diff --git a/tests/testthat/test_table_functions.R b/tests/testthat/test_table_functions.R
@@ -2,6 +2,7 @@ data(data_fungi)
 data(enterotype)
 
 test_that("tax_datatable function works fine with data_fungi dataset", {
+  skip_on_os("windows")
   expect_silent(taxdt <- tax_datatable(data_fungi))
   expect_s3_class(taxdt, "datatables")
   expect_silent(taxdt <- tax_datatable(data_fungi, taxonomic_level = 1:2))
@@ -12,6 +13,7 @@ test_that("tax_datatable function works fine with data_fungi dataset", {
 
 
 test_that("tax_datatable function works fine with enterotype dataset", {
+  skip_on_os("windows")
   expect_silent(tax_datatable(enterotype))
   expect_s3_class(tax_datatable(enterotype), "datatables")
   expect_silent(tax_datatable(enterotype, modality = enterotype@sam_data$SeqTech))

diff --git a/tests/testthat/test_targets.R b/tests/testthat/test_targets.R
@@ -78,6 +78,7 @@ data_fungi_test@otu_table[10, ] <-
   rep(0, ncol(data_fungi_test@otu_table))
 
 test_that("track_wkflow function works fine", {
+  skip_on_os("windows")
   expect_message(track_wkflow(list(
     unlist(list_fastq_files("inst/extdata/")), data_fungi, enterotype
   )))
@@ -119,6 +120,7 @@ derep_R_001 <-
     "inst/extdata/ex_R2_001.fastq.gz"
   ))
 test_that("track_wkflow_samples function works fine with object of class matrix, dada and derep", {
+  skip_on_os("windows")
   expect_s3_class(track_wkflow(
     list(
       data_fungi@otu_table,

diff --git a/vignettes/MiscMetabar.Rmd b/vignettes/MiscMetabar.Rmd
@@ -29,7 +29,7 @@ knitr::opts_chunk$set(
 For an introduction to metabarcoding in R, Please visite the [state of the field](https://adrientaudiere.github.io/MiscMetabar/articles/states_of_fields_in_R.html) vignettes. The [import, export and track](https://adrientaudiere.github.io/MiscMetabar/articles/import_export_track.html) vignette explains how import and export `phyloseq` object. Its also show how to summarize useful information (number of sequences, samples and clusters) accross bioinformatic pipelines. 
 
 If you are interested in ecological metrics, see the vignettes describing [alpha-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/alpha-div.html) and [beta-diversity](https://adrientaudiere.github.io/MiscMetabar/articles/beta-div.html) analysis. 
-The vignette [filter taxa and samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html) describes some data-filtering processes using MiscMetabar and the [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html) tutorial introduces the different way of clustering already-clustered OTU/ASV. The vignette [tengeler]() explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions.
+The vignette [filter taxa and samples](https://adrientaudiere.github.io/MiscMetabar/articles/filter.html) describes some data-filtering processes using MiscMetabar and the [reclustering](https://adrientaudiere.github.io/MiscMetabar/articles/Reclustering.html) tutorial introduces the different way of clustering already-clustered OTU/ASV. The vignette [tengeler](https://adrientaudiere.github.io/MiscMetabar/articles/tengeler.html) explore the dataset from Tengeler et al. (2020) using some MiscMetabar functions.
 
 For developers, I also wrote a vignette describing som [rules of codes](https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html). 
 
@@ -62,10 +62,10 @@ sankey_pq(gp, taxa = c(1:5))
 ```
 
 
-### Circle for visualize distribution of taxa in function of samples variables
+### Upset plot for visualize distribution of taxa in function of samples variables
 
 ```{r}
-circle_pq(gp, "SampleType", taxa = "Class")
+upset_pq(gp, "SampleType", taxa = "Class")
 ```