move to using pkg sys when ready

[jeroen]

The problems with sys should be fixed now as of version 1.1 on CRAN.

[sckott]

thanks

[sckott]

@jeroenooms not sure what's going wrong,

trying this, but:

install from sys branch, then

library(sys)
library(phylocomr)

tf <- tempfile()
pf <- tempfile()
cat(c("campanulaceae/lobelia/lobelia_conferta", "cyperaceae/mapania/mapania_africana", "amaryllidaceae/narcissus/narcissus_cuatrecasasii"), file = tf, sep = "\n")
cat("(((((eliea_articulata,homalanthus_populneus)malpighiales,rosa_willmottiae),((macrocentrum_neblinae,qualea_clavata),hibiscus_pohlii)malvids),(((lobelia_conferta,((millotia_depauperata,(layia_chrysanthemoides,layia_pentachaeta)layia),senecio_flanaganii)asteraceae)asterales,schwenkia_americana),tapinanthus_buntingii)),(narcissus_cuatrecasasii,mapania_africana))poales_to_asterales;", file = pf, sep = "\n")

# check they're there
file.exists(tf, pf)
readLines(tf)
readLines(pf)

args <- sprintf("-t %s -f %s", tf, pf)
path <- file.path(
  system.file("bin", .Platform$r_arch, package = "phylocomr"), "phylomatic")
out <- rawConnection(raw(0), "r+")
(res <- sys::exec_wait(path, args, std_out = out))
#> 8
rawToChar(rawConnectionValue(out))
#> "Cannot open phylogeny file\n"

[jeroen]

The args argument must be a character vector with args. Don't concat it into a string. Then it should work.

args <- c("-t", tf, "-f", pf)

[sckott]

interesting, ok. why wouldn't it also work as one string? just curious

[jeroen]

Actually I thought that system2 works the same way, but apparently it doesn't. The args map directly to the argument vector from the executable. So in your case the executable would be run with only one big argument, containing spaces...

[jeroen]

Als you might be able to simplify the code using exec_internal:

tf <- tempfile()
pf <- tempfile()
cat(c("campanulaceae/lobelia/lobelia_conferta", "cyperaceae/mapania/mapania_africana", "amaryllidaceae/narcissus/narcissus_cuatrecasasii"), file = tf, sep = "\n")
cat("(((((eliea_articulata,homalanthus_populneus)malpighiales,rosa_willmottiae),((macrocentrum_neblinae,qualea_clavata),hibiscus_pohlii)malvids),(((lobelia_conferta,((millotia_depauperata,(layia_chrysanthemoides,layia_pentachaeta)layia),senecio_flanaganii)asteraceae)asterales,schwenkia_americana),tapinanthus_buntingii)),(narcissus_cuatrecasasii,mapania_africana))poales_to_asterales;", file = pf, sep = "\n")

# check they're there
file.exists(tf, pf)
readLines(tf)
readLines(pf)

args <- c("-t", tf, "-f", pf)
path <- file.path(
  system.file("bin", .Platform$r_arch, package = "phylocomr"), "phylomatic")
out <- sys::exec_internal(path, args, error = FALSE)
rawToChar(out$stdout)

[sckott]

Thanks, that works.

Right, exec_internal should be easier

[sckott]

fixed via #7