Adds @export to internal S3 methods so that they are registered & fou…

…nd properly. We were getting hosed during unit testing because R v4.0.x chnaged the way S3 generics are found, and we now have to add an `@export` roxygen tag to internal S3 functions for things to work like before. Here is a more thorough / accurate discussion of the topic and suggested fix which was implemented in this commit: r-lib/devtools#2293
facilebio · Dec 1, 2020 · df12f38 · df12f38
1 parent cd8a1d4
commit df12f38
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diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -31,10 +31,10 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Setup R
-        uses: r-lib/actions/setup-r@2fac31217e602dd30286b4c984a0ccf1afb18cbd
-        # uses: r-lib/actions/setup-r@master
-        # with:
-        #   install-r: false
+        # uses: r-lib/actions/setup-r@2fac31217e602dd30286b4c984a0ccf1afb18cbd
+        uses: r-lib/actions/setup-r@v1
+        with:
+          install-r: false
 
       # pandoc is already installed in the docker container
       # - uses: r-lib/actions/setup-pandoc@master

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: FacileData
 Type: Package
 Title: A fluent API for accessing multi-assay high-throughput genomics data
-Version: 0.11.7
+Version: 0.11.8
 Authors@R: c(
     person("Steve", "Lianoglou", , "lianoglou@dnli.com", c("aut", "cre"),
       comment = c(ORCID = "0000-0002-0924-1754")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,11 +3,16 @@
 S3method("fds<-",data.frame)
 S3method("fds<-",default)
 S3method("fds<-",tbl)
+S3method(adata,DGEList)
+S3method(adata,EList)
+S3method(adata,ExpressionSet)
+S3method(adata,SummarizedExperiment)
 S3method(anti_join,facile_frame)
 S3method(arrange,facile_frame)
 S3method(as.DGEList,FacileDataSet)
 S3method(as.DGEList,data.frame)
 S3method(as.DGEList,facile_frame)
+S3method(as.DGEList,matrix)
 S3method(as.DGEList,tbl)
 S3method(as.ExpressionSet,FacileDataSet)
 S3method(as.ExpressionSet,data.frame)
@@ -28,8 +33,15 @@ S3method(covariate_definitions,FacileDataSet)
 S3method(default_assay,FacileDataSet)
 S3method(default_assay,default)
 S3method(distinct,facile_frame)
+S3method(ds_annot,ExpressionSet)
+S3method(ds_annot,SummarizedExperiment)
+S3method(ds_annot,default)
 S3method(facet_frame,FacileDataSet)
 S3method(facet_frame,default)
+S3method(fdata,DGEList)
+S3method(fdata,EList)
+S3method(fdata,ExpressionSet)
+S3method(fdata,SummarizedExperiment)
 S3method(fds,FacileDataStore)
 S3method(fds,default)
 S3method(features,FacileDataSet)
@@ -41,6 +53,7 @@ S3method(fetch_assay_score,default)
 S3method(fetch_custom_sample_covariates,FacileDataSet)
 S3method(fetch_custom_sample_covariates,default)
 S3method(fetch_feature_info,FacileDataSet)
+S3method(fetch_feature_info,default)
 S3method(fetch_sample_covariates,FacileDataSet)
 S3method(fetch_sample_covariates,default)
 S3method(fetch_sample_covariates,facile_frame)
@@ -67,6 +80,10 @@ S3method(name,FacileDataSet)
 S3method(organism,FacileDataSet)
 S3method(organism,default)
 S3method(organism,facile_frame)
+S3method(pdata,DGEList)
+S3method(pdata,EList)
+S3method(pdata,ExpressionSet)
+S3method(pdata,SummarizedExperiment)
 S3method(pdata_metadata,DGEList)
 S3method(pdata_metadata,EList)
 S3method(pdata_metadata,ExpressionSet)
@@ -89,6 +106,7 @@ S3method(ungroup,facile_frame)
 S3method(with_assay_covariates,data.frame)
 S3method(with_assay_covariates,facile_frame)
 S3method(with_assay_data,data.frame)
+S3method(with_assay_data,default)
 S3method(with_assay_data,facile_frame)
 S3method(with_assay_data,tbl)
 S3method(with_feature_info,data.frame)

diff --git a/R/api.R b/R/api.R
@@ -404,6 +404,8 @@ fetch_feature_info <- function(x, feature_type, feature_ids = NULL, ...) {
   UseMethod("fetch_feature_info", x)
 }
 
+#' @noRd
+#' @export
 fetch_feature_info.default <- function(x, feature_type, feature_ids = NULL, ...) {
   stop("Implement fetch_feature_info for class: ", class(x)[1L])
 }
@@ -581,6 +583,8 @@ with_assay_data <- function(x, features, assay_name = NULL,
   UseMethod("with_assay_data", x)
 }
 
+#' @noRd
+#' @export
 with_assay_data.default <- function(x, features, assay_name = NULL,
                                     normalized = TRUE, aggregate = FALSE,
                                     aggregate.by = "ewm",

diff --git a/R/as.BiocAssayContainers.R b/R/as.BiocAssayContainers.R
@@ -61,6 +61,7 @@ as.DGEList <- function(x, ...) {
 }
 
 #' @noRd
+#' @export
 #' @method as.DGEList matrix
 #' @rdname as.BiocContainer
 #' @importFrom edgeR DGEList calcNormFactors
@@ -164,8 +165,9 @@ as.DGEList.matrix <- function(x, covariates = TRUE, feature_ids = NULL,
   is.neg <- which(x < 0, arr.ind = TRUE)
   if (nrow(is.neg)) x[is.neg] <- x[is.neg] * -1
 
-  y <- DGEList(x, genes = genes, lib.size = sample.stats[["libsize"]],
-               norm.factors = sample.stats[["normfactor"]])
+  y <- DGEList(x, genes = genes, lib.size = sample.stats[["libsize"]])
+  # This avoids the warning when norm factors don't multiply to 1
+  y$samples$norm.factors <- sample.stats[["normfactor"]]
 
   y$samples <- cbind(
     y$samples,

diff --git a/R/as.FacileDataSet.R b/R/as.FacileDataSet.R
@@ -302,6 +302,9 @@ as.FacileDataSet.list <- function(x, path, assay_name, assay_type,
 #' no such slot, unfortunately, and thus gets the default. SE has a
 #' metadata slot and can provide url and description. eSet just has
 #' a character annotation and can provide a description.
+#'
+#' This is an internal helper function.
+#'
 #' @param x SummarizedExperiment, ExpressionSet or DGEList
 #' @param validate single logical, check results
 #' @param meta a list of description stuff for the dataset, this can act to
@@ -311,6 +314,8 @@ ds_annot <- function(x, meta = NULL, validate = FALSE, ...) {
   UseMethod("ds_annot")
 }
 
+#' @noRd
+#' @export
 ds_annot.SummarizedExperiment <- function(x, meta = NULL, validate = FALSE,
                                           ...) {
   ns4 <- tryCatch(loadNamespace("S4Vectors"), error = function(e) NULL)
@@ -321,12 +326,16 @@ ds_annot.SummarizedExperiment <- function(x, meta = NULL, validate = FALSE,
   out
 }
 
+#' @noRd
+#' @export
 ds_annot.ExpressionSet <- function(x, meta = NULL, validate = FALSE, ...) {
   out <- .merge_ds_annot(NULL, meta)
   if (validate) .ds_annot_validate(out)
   out
 }
 
+#' @noRd
+#' @export
 ds_annot.default <- function(x, meta = NULL, validate = FALSE, ...) {
   out <- .merge_ds_annot(NULL, meta)
   if (validate) .ds_annot_validate(out)
@@ -359,35 +368,45 @@ ds_annot.default <- function(x, meta = NULL, validate = FALSE, ...) {
 
 #' BioC-container specific fData extraction functions
 #'
-#' not for export
 #' @param x SummarizedExperiment, ExpressionSet or DGEList
 #' @param validate single logical, check results
 #' @param ... additional args (ignored for now)
 fdata <- function(x, validate = FALSE, ...) {
   UseMethod("fdata")
 }
+
+#' @noRd
+#' @export
 fdata.SummarizedExperiment <- function(x, validate = FALSE, ...) {
   ns <- tryCatch(loadNamespace("SummarizedExperiment"), error = function(e) NULL)
   if (is.null(ns)) stop("SummarizedExperiment required")
   ns4 <- tryCatch(loadNamespace("S4Vectors"), error = function(e) NULL)
   if (is.null(ns4)) stop("S4Vectors required")
 
-  # out <- ns$as.data.frame(ns$mcols(x))
-  out <- ns4$as.data.frame.DataTable(ns$rowData(x))
+  out <- ns4$.as.data.frame.DataFrame(ns$rowData(x))
   if (validate) validate.fdata(out, ...) else out
 }
+
+#' @noRd
+#' @export
 fdata.ExpressionSet <- function(x, validate = FALSE, ...) {
   ns <- tryCatch(loadNamespace("Biobase"), error = function(e) NULL)
   if (is.null(ns)) stop("Biobase required")
 
   out <- ns$fData(x)
   if (validate) validate.fdata(out, ...) else out
 }
+
+#' @noRd
+#' @export
 fdata.DGEList <- function(x, validate = FALSE, ...) {
   # stopifnot(requireNamespace("edgeR", quietly = TRUE))
   out <- x$genes
   if (validate) validate.fdata(out, ...) else out
 }
+
+#' @noRd
+#' @export
 fdata.EList <- function(x, validate = FALSE, ...) {
   out <- x$genes
   if (validate) validate.fdata(out, ...) else out
@@ -425,33 +444,37 @@ validate.fdata <- function(x, ...) {
 
 #' Bioc-container specific pData extraction functions
 #'
-#' not for export
+#' This is an internal function, but exported so it is registered and found
+#' post R 4.0
 #' @param x SummarizedExperiment, ExpressionSet or DGEList
 #' @param ... additional args, ignored for now
 pdata <- function(x, covariate_metadata = NULL, ...) {
-  UseMethod("pdata")
+  UseMethod("pdata", x)
 }
 
 #' @noRd
+#' @export
 pdata.SummarizedExperiment <- function(x, covariate_metadata = NULL,  ...) {
   ns <- tryCatch(loadNamespace("SummarizedExperiment"), error = function(e) NULL)
   if (is.null(ns)) stop("SummarizedExperiment required")
   ns4 <- tryCatch(loadNamespace("S4Vectors"), error = function(e) NULL)
   if (is.null(ns4)) stop("S4Vectors required")
 
   df <- ns$colData(x)
-  ds <- ns4$as.data.frame.DataTable(df)
+  ds <- ns4$.as.data.frame.DataFrame(df)
   validate.pdata(ds, ...)
 }
 
 #' @noRd
+#' @export
 pdata.ExpressionSet <- function(x, covariate_metadata = NULL,  ...) {
   ns <- tryCatch(loadNamespace("Biobase"), error = function(e) NULL)
   if (is.null(ns)) stop("Biobase required")
   validate.pdata(ns$pData(x), ...)
 }
 
 #' @noRd
+#' @export
 pdata.DGEList <- function(x, covariate_metadata = NULL,  ...) {
   # stopifnot(requireNamespace("edgeR", quietly = TRUE))
   ignore.cols <- c("lib.size", "norm.factors")
@@ -463,10 +486,12 @@ pdata.DGEList <- function(x, covariate_metadata = NULL,  ...) {
 }
 
 #' @noRd
+#' @export
 pdata.EList <- function(x, covariate_metadata = NULL,  ...) {
   validate.pdata(x$targets, ...)
 }
 
+#' @noRd
 validate.pdata <- function(x, ...) {
   x
 }
@@ -530,13 +555,15 @@ pdata_metadata.EList <- function(x, ...) {
 #' Bioc-container specific assay data extraction functions
 #'
 #' Get assay matrix
+#'
 #' @param x SummarizedExperiment, ExpressionSet or DGEList
 #' @param ... additional args, ignored for now
 adata <- function(x, assay = NULL, ...) {
-  UseMethod("adata")
+  UseMethod("adata", x)
 }
 
 #' @noRd
+#' @export
 adata.SummarizedExperiment <- function(x, assay = NULL, ...) {
   ns <- tryCatch(loadNamespace("SummarizedExperiment"), error = function(e) NULL)
   if (is.null(ns)) stop("SummarizedExperiment required")
@@ -549,6 +576,7 @@ adata.SummarizedExperiment <- function(x, assay = NULL, ...) {
 }
 
 #' @noRd
+#' @export
 adata.ExpressionSet <- function(x, assay = NULL, ...) {
   ns <- tryCatch(loadNamespace("Biobase"), error = function(e) NULL)
   if (is.null(ns)) stop("Biobase required")
@@ -561,13 +589,15 @@ adata.ExpressionSet <- function(x, assay = NULL, ...) {
 }
 
 #' @noRd
+#' @export
 adata.DGEList <- function(x, assay = NULL, ...) {
   # stopifnot(requireNamespace("edgeR", quietly = TRUE))
   # DGEList only has one assay
   x$counts
 }
 
 #' @noRd
+#' @export
 adata.EList <- function(x, assay = NULL, ...) {
   # EList only has one assay
   x[["E"]]

diff --git a/R/assay-data.R b/R/assay-data.R
@@ -115,7 +115,7 @@ fetch_assay_data.FacileDataSet <- function(x, features, samples = NULL,
 
 #' @export
 #' @noRd
-fetch_assay_data.facile_frame <- function(x, features, samples = NULL,
+fetch_assay_data.facile_frame <- function(x, features = NULL, samples = NULL,
                                           assay_name = NULL,
                                           normalized = FALSE,
                                           batch = NULL, main = NULL,

diff --git a/R/biocbox.R b/R/biocbox.R
@@ -22,7 +22,7 @@ biocbox.FacileDataStore <- function(x, class = NULL, assay_name = NULL,
 #' DGEList lib.size calculated from the data that made its way into the DGEList)
 #'
 #' @export
-#'
+#' @rdname biocbox
 #' @param sample_covariates If `NULL` (default), all sample covariates will
 #'   be included over samples in x. If a data.frame, we will treat the
 #'   extra columns as custom covariates, and include them in the outgoing

diff --git a/man/FacileData-package.Rd b/man/FacileData-package.Rd
diff --git a/man/biocbox.Rd b/man/biocbox.Rd
diff --git a/man/ds_annot.Rd b/man/ds_annot.Rd
diff --git a/man/fdata.Rd b/man/fdata.Rd