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#' from a MAF instance create a key with ref, alt and positional information,
#' return in a data.frame with key and gene symbol
#' @param mafinst instance of S4 class MAF from maftools
#' @param altfield character(1) name of field to use for mutation substitution
#' @param donorfield character(1) name of field to use for donor
#' @param uniprot_ok character() or NULL, defaults to NULL, if non-NULL, data to be returned will
#' only include records with UNIPROT id matching an element in this vector
#' @export
maf2key = function(mafinst, altfield="Tumor_Seq_Allele2", donorfield="Tumor_Sample_Barcode",

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---
title: "Triggers a curl/httr segfault during R CMD build"
author: Hervé Pagès
output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2
vignette: >
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}

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> sessionInfo()
R version 4.4.1 Patched (2024-09-30 r87215)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so 
LAPACK: /usr/local/lib/R/lib/libRlapack.so;  LAPACK version 3.12.0

locale:

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##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocFileCache
###
##############################################################################
##############################################################################

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library(shiny)
library(xenLite)
library(SpatialExperiment)

what = "LUAD"

  ui = fluidPage(
   sidebarLayout(
    sidebarPanel(
     uiOutput("topbox"),

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setup:

> options(repos=c(BioCsoft="https://bioc.r-universe.dev", CRAN="https://cloud.r-project.org"))

> getOption("repos")
                     BioCsoft                          CRAN 
"https://bioc.r-universe.dev" "https://cloud.r-project.org" 

> install.packages("impute")
Installing package into ‘/Users/papa/Library/R/arm64/4.4/library’

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library(plotly)
library(ggplot2)
library(XenSCE)
if (!exists("gbm")) load("gbm.rda")

print.xen_ggprep = function(x, ...) {
  cat(sprintf("xen_ggprep instance for %d cells with %d cell boundary vertices.\n", ncol(x$sampd), nrow(x$bounds)))
}

ggprep_seg = function(xsce, xlim=c(5800,6200), ylim=c(6300, 6700), show_tx=TRUE) {

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library(plotly)
library(ggplot2)
library(XenSCE)
if (!exists("gbm")) load("gbm.rda")
plotly_seg = function(xsce, xlim=c(5800,6000), ylim=c(6300, 6500), show_tx=TRUE) {
  bounds = getCellBoundaries(xsce)
  bounds = bounds[bounds$vertex_x > xlim[1] &
      bounds$vertex_x < xlim[2] & bounds$vertex_y > ylim[1] & bounds$vertex_y < ylim[2],]
  c4 <- as.data.frame(bounds)
  #ggplot(c4, aes(x=vertex_x, y=vertex_y, group=cell_id)) + geom_path() -> pas

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library(shiny)
library(ParquetDataFrame)
library(XenSCE)

if (!exists("gbm")) load("gbm.rda")

ui = fluidPage(
 sidebarLayout(
  sidebarPanel(
   helpText("view gbm"),

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get_bioc_packagelist = function(rel = "RELEASE_3_19") {
 system("git clone https://git.bioconductor.org/admin/manifest")
 owd = getwd()
 setwd("manifest")
 on.exit(setwd(owd))
 system(paste("git checkout ", rel))
 proc_software.txt = function() {
  x = readLines("software.txt")[-1]  # first line is comment
  nn = which(nchar(x)==0)
  tmp = x[-nn]