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## BiocManager::install("BiocCheck")

getAPIcalls <- function(packageDir) {
    annv <- BiocCheck:::parseFiles(packageDir)
    annv <- annv[endsWith(dirname(names(annv)), "R")]

    funnames <- c("Terra", "Rawls", "Leonardo", "Leo", "Dockstore")
    reslist <- replicate(length(funnames), annv, simplify = FALSE)
    names(reslist) <- funnames

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---
title: "Bioconductor Release Schedule"
date: "2024-04-11"
html_output:
  BiocStyle::html_output
---

## Dependencies

```{r}

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hasValueSection <- function(manpage) {
    rd <- tools::parse_Rd(manpage)
    type <- BiocCheck:::docType(rd)
    if (identical(type, "data"))
        return(TRUE)
    tags <- tools:::RdTags(rd)
    if ("\\usage" %in% tags && (!"\\value" %in% tags))
        return(FALSE)
    value <- NULL
    if ("\\value" %in% tags)

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library(shiny)
library(purrr)
library(DT)
data("mtcars")

miniapp <- function(...) {

ids <- paste0("Tab2_Column", 1:5, "_Variable")
vchoices <- names(mtcars)

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---
title: "Review of trtools"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Test code to connect to clinical mart is showing an error:

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# gists/12f99b49d6c009f80ff49a8823ad47ea/readproto.R

library(RProtoBuf)

setwd("~/gh")
## git clone git@github.com:phenopackets/phenopacket-schema.git
## git submodule update --init --recursive

setwd("~/gh/phenopacket-schema/src/main/proto")

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library(rvest)
library(xml2)
library(lubridate)
library(yaml)

buildrep <- xml2::read_html("https://bioconductor.org/checkResults/")
html_text(html_nodes(buildrep, "li"))

nodes <- html_nodes(buildrep, "div")[-1:-2]
bioc_names <- html_text(html_nodes(nodes, "h3"))

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library(BiocPkgTools)
library(dplyr)

dev <- biocBuildReport(version = BiocManager::version(), stage.timings = TRUE)

dev[["elapsed"]] <- as.numeric(
    vapply(strsplit(dev[["EllapsedTime"]], " "), `[`, character(1L), 1L)
)

dev |> group_by(stage, node) |> summarize(n = n())

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metrics_file <- "pbmc_granulocyte_sorted_3k_per_barcode_metrics.csv"
bm <- read.csv(metrics_file)
dim(bm)

## all unique barcodes
identical(length(unique(bm$atac_barcode)), length(bm$atac_barcode))

abcs <- bm[, "atac_barcode", drop = FALSE]

# with col.names = TRUE

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# setwd("~/ASM19595v2")
# dir.create(testdir <- normalizePath("~/ASM19595v2/"))
# setwd(testdir)
testfile <- normalizePath("./genome_assemblies_genome_fasta.tar")
wd <- dirname(testfile)
download.file("https://www.ncbi.nlm.nih.gov/projects/r_gencoll/ftp_service/nph-gc-ftp-service.cgi/?HistoryId=MCID_61391356369bba150d3809be&QueryKey=1&ReleaseType=RefSeq&FileType=GENOME_FASTA&Flat=true", testfile)
untar(testfile)
fastazip <- list.files(wd, recursive = TRUE, pattern = "fna.gz$")
library(BSgenome)
fasta.seqlengths(fastazip)