Description
I am getting the following error when I use the ph_phylomatic function in phylocomr;
tree_arctic<-ph_phylomatic(taxa = taxa_list_short, phylo = zanne2014)
Error: call to 'phylomatic' failed with status -1073740940
Here is my code. There is a list of 232 taxa (family/genus/genus_species) in species_list$family_genus_species (attached):
library("phylocomr")
library("ape")
zanne2014 <- ape::read.tree(text=brranching::phylomatic_trees[['zanne2014']])
species_list<-read.csv(file="species_list.csv",header = TRUE, stringsAsFactors=FALSE)
taxa_list<-unique(species_list$family_genus_species)
tree_arctic<-ph_phylomatic(taxa = taxa_list, phylo = zanne2014)
but if I use a much short taxa list it works and the phylogeny is created:
taxa_list_short<-taxa_list[1:6]
tree_arctic<-ph_phylomatic(taxa = taxa_list_short, phylo = zanne2014)
I am wondering if it is related to this issue ropensci/brranching#17 where this is mentioned "I traced down the error and in my case it lies within the phylomatic function. For some reason, the output called out is truncated. It can contain 8095 characters at maximum. If I add too many species, the output just cuts somewhere in the middle of a species name, and the final ";" is missing. This forces read.newick into an eternal loop." BTW I did also try using phylomatic_local in brranching and it just disappears down a black and never returns.
Session info is:
sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
Session Info
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] brranching_0.7.0 taxize_0.9.99 ape_5.6-2 phylocomr_0.3.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 lattice_0.20-45
[3] prettyunits_1.1.1 ps_1.6.0
[5] zoo_1.8-9 rprojroot_2.0.2
[7] foreach_1.5.2 utf8_1.2.2
[9] R6_2.5.1 plyr_1.8.6
[11] sys_3.4 phytools_1.0-1
[13] coda_0.19-4 pillar_1.7.0
[15] rlang_1.0.2 curl_4.3.2
[17] uuid_1.0-4 data.table_1.14.2
[19] phangorn_2.8.1 callr_3.7.0
[21] Matrix_1.4-0 combinat_0.0-8
[23] desc_1.4.1 stringr_1.4.0
[25] igraph_1.2.11 compiler_4.1.1
[27] numDeriv_2016.8-1.1 pkgconfig_2.0.3
[29] mnormt_2.0.2 pkgbuild_1.3.1
[31] tmvnsim_1.0-2 conditionz_0.1.0
[33] tidyselect_1.1.2 tibble_3.1.4
[35] httpcode_0.3.0 expm_0.999-6
[37] quadprog_1.5-8 codetools_0.2-18
[39] reshape_0.8.8 fansi_0.5.0
[41] crayon_1.5.0 dplyr_1.0.8
[43] withr_2.5.0 MASS_7.3-55
[45] crul_1.2.0 grid_4.1.1
[47] nlme_3.1-155 jsonlite_1.8.0
[49] lifecycle_1.0.1 magrittr_2.0.1
[51] cli_3.0.1 stringi_1.7.6
[53] cachem_1.0.6 fs_1.5.0
[55] remotes_2.4.2 scatterplot3d_0.3-41
[57] testthat_3.0.4 xml2_1.3.3
[59] ellipsis_0.3.2 generics_0.1.2
[61] vctrs_0.3.8 fastmatch_1.1-3
[63] iterators_1.0.14 tools_4.1.1
[65] bold_1.2.0 glue_1.4.2
[67] purrr_0.3.4 maps_3.4.0
[69] plotrix_3.8-2 processx_3.5.2
[71] pkgload_1.2.4 parallel_4.1.1
[73] fastmap_1.1.0 memoise_2.0.1
[75] clusterGeneration_1.3.7