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ropensci / phylocomr

Phylocom R interface
https://docs.ropensci.org/phylocomr
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Error: call to 'phylomatic' failed with status -1073740940 #32

Open zedpanch opened 2 years ago

zedpanch commented 2 years ago

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 https://github.com/ropensci/brranching/issues/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 [species_list.csv](https://github.com/ropensci/phylocomr/files/8352527/species_list.csv)
ywckusuma commented 2 months ago

Hi, I do have the same problem every time I run phylomatic I have this problem:

com_phylo <- ph_phylomatic(com_str, ferry2015) Error: call to 'phylomatic' failed with status -1073740940 sessioninfo::session_info() ─ Session info ─────────────────────────────────────────────────────────────────────────────── setting value version R version 4.4.1 (2024-06-14 ucrt) os Windows 11 x64 (build 22631) system x86_64, mingw32 ui RStudio language (EN) collate English_United States.utf8 ctype English_United States.utf8 tz Asia/Jakarta date 2024-08-31 rstudio 2024.04.2+764 Chocolate Cosmos (desktop) pandoc NA

─ Packages ─────────────────────────────────────────────────────────────────────────────────── package version date (UTC) lib source ape 5.8 2024-04-11 [1] CRAN (R 4.4.0) brranching 0.7.1 2024-08-30 [1] Github (ropensci/brranching@efd089f) cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0) cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.1) clusterGeneration 1.3.8 2023-08-16 [1] CRAN (R 4.4.1) coda 0.19-4.1 2024-01-31 [1] CRAN (R 4.4.1) codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.1) combinat 0.0-8 2012-10-29 [1] CRAN (R 4.4.0) conditionz 0.1.0 2019-04-24 [1] CRAN (R 4.4.1) crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.1) crul 1.5.0 2024-07-19 [1] CRAN (R 4.4.1) curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0) data.table 1.16.0 2024-08-27 [1] CRAN (R 4.4.1) DEoptim 2.2-8 2022-11-11 [1] CRAN (R 4.4.1) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.0) digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0) doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.4.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.0) expm 1.0-0 2024-08-19 [1] CRAN (R 4.4.1) fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0) fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.4.0) foreach 1.5.2 2022-02-02 [1] CRAN (R 4.4.0) fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0) generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0) htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0) httpcode 0.3.0 2020-04-10 [1] CRAN (R 4.4.1) httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0) igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.0) iterators 1.0.14 2022-02-05 [1] CRAN (R 4.4.0) jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0) later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0) lattice 0.22-6 2024-03-20 [2] CRAN (R 4.4.1) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) maps 3.4.2 2023-12-15 [1] CRAN (R 4.4.0) MASS 7.3-60.2 2024-04-26 [2] CRAN (R 4.4.1) Matrix 1.7-0 2024-04-26 [2] CRAN (R 4.4.1) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0) mime 0.12 2021-09-28 [1] CRAN (R 4.4.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0) mnormt 2.1.1 2022-09-26 [1] CRAN (R 4.4.0) nlme 3.1-164 2023-11-27 [2] CRAN (R 4.4.1) numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.4.0) optimParallel 1.0-2 2021-02-11 [1] CRAN (R 4.4.1) phangorn 2.11.1 2023-01-23 [1] CRAN (R 4.4.1) phylocomr 0.3.4 2023-04-22 [1] CRAN (R 4.4.1) phytools 2.3-0 2024-06-13 [1] CRAN (R 4.4.1) pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.4.0) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.0) promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0) quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.4.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0) remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0) rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0) rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0) scatterplot3d 0.3-44 2023-05-05 [1] CRAN (R 4.4.0) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.1) shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0) stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0) sys 3.4.2 2023-05-23 [1] CRAN (R 4.4.0) taxize 0.9.100.1 2024-08-26 [1] CRAN (R 4.4.1) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.0) usethis 2.2.3 2024-02-19 [1] CRAN (R 4.4.0) uuid 1.2-1 2024-07-29 [1] CRAN (R 4.4.1) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0) xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0) zoo 1.8-12 2023-04-13 [1] CRAN (R 4.4.1)

[1] C:/Users/Yayan Kusuma/AppData/Local/R/win-library/4.4 [2] C:/Program Files/R/R-4.4.1/library

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Last two year, it is so easy to install phylocomr and use it. It is now very challenging to solve this problem. I try to use mac as well, and I do have similar problem with different problem code.

Is there any way to solve this?

I like to use phylocomr to construct community phylogeny based on species list.