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Description
Hi,
I am trying to calculate Faith's PD in a sample of avian species.
When i run this code
library(ape)
library(readxl)
library(picante)
library(phylocomr)
samplepd <- read_excel('~/R_library/chapter4/sample_ph_pd.xlsx')
consensus_newick <- read.tree('~/R_library/chapter4/consensus_newick.txt')
samplepd <- as.data.frame(samplepd)
ph_pd(samplepd, consensus_newick)I get this error:
Error: Program '/home/jovyan/R_library/phylocomr/bin//phylocom' terminated by SIGNAL (Segmentation fault)These are my files:
consensus_newick.txt
sample_ph_pd.xlsx
An this is my session info:
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.1.3 (2022-03-10)
os Ubuntu 22.04.2 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2023-09-15
rstudio 2022.07.1+554 Spotted Wakerobin (server)
pandoc 2.19.2 @ /opt/conda/bin/pandoc
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
ape * 5.7-1 2023-03-13 [1] CRAN (R 4.1.3)
cachem 1.0.6 2021-08-19 [2] CRAN (R 4.1.1)
callr 3.7.2 2022-08-22 [2] CRAN (R 4.1.3)
cellranger 1.1.0 2016-07-27 [2] CRAN (R 4.1.2)
cli 3.4.1 2022-09-23 [2] CRAN (R 4.1.3)
cluster 2.1.4 2022-08-22 [1] CRAN (R 4.1.3)
clusterGeneration 1.3.8 2023-08-16 [1] CRAN (R 4.1.3)
coda 0.19-4 2020-09-30 [1] CRAN (R 4.1.3)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.1.0)
combinat 0.0-8 2012-10-29 [1] CRAN (R 4.1.3)
crayon 1.5.1 2022-03-26 [2] CRAN (R 4.1.2)
curl 4.3.2 2021-06-23 [2] CRAN (R 4.1.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.1.3)
digest 0.6.29 2021-12-01 [2] CRAN (R 4.1.1)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.1.3)
ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.1.0)
expm 0.999-7 2023-01-09 [1] CRAN (R 4.1.3)
fansi 1.0.3 2022-03-24 [2] CRAN (R 4.1.2)
fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.1.0)
fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.1.3)
foreach 1.5.2 2022-02-02 [2] CRAN (R 4.1.2)
fs 1.5.2 2021-12-08 [2] CRAN (R 4.1.3)
generics 0.1.3 2022-07-05 [2] CRAN (R 4.1.3)
glue 1.6.2 2022-02-24 [2] CRAN (R 4.1.2)
htmltools 0.5.3 2022-07-18 [2] CRAN (R 4.1.3)
htmlwidgets 1.5.4 2021-09-08 [2] CRAN (R 4.1.1)
httpuv 1.6.6 2022-09-08 [2] CRAN (R 4.1.3)
igraph 1.5.1 2023-08-10 [1] CRAN (R 4.1.3)
iterators 1.0.14 2022-02-05 [2] CRAN (R 4.1.2)
later 1.2.0 2021-04-23 [2] CRAN (R 4.1.0)
lattice * 0.20-45 2021-09-22 [2] CRAN (R 4.1.1)
lifecycle 1.0.2 2022-09-09 [2] CRAN (R 4.1.3)
magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.1.3)
maps * 3.4.1 2022-10-30 [1] CRAN (R 4.1.3)
MASS 7.3-58.1 2022-08-03 [2] CRAN (R 4.1.3)
Matrix 1.4-1 2022-03-23 [2] CRAN (R 4.1.2)
memoise 2.0.1 2021-11-26 [2] CRAN (R 4.1.1)
mgcv 1.8-40 2022-03-29 [2] CRAN (R 4.1.3)
mime 0.12 2021-09-28 [2] CRAN (R 4.1.1)
miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.1.0)
mnormt 2.1.1 2022-09-26
90FD
[1] CRAN (R 4.1.3)
nlme * 3.1-159 2022-08-09 [2] CRAN (R 4.1.3)
numDeriv 2016.8-1.1 2019-06-06 [2] CRAN (R 4.1.0)
optimParallel 1.0-2 2021-02-11 [1] CRAN (R 4.1.3)
permute * 0.9-7 2022-01-27 [1] CRAN (R 4.1.3)
phangorn 2.11.1 2023-01-23 [1] CRAN (R 4.1.3)
phylocomr * 0.3.4 2023-04-22 [1] CRAN (R 4.1.3)
phytools * 1.9-16 2023-07-14 [1] CRAN (R 4.1.3)
picante * 1.8.2 2020-06-10 [1] CRAN (R 4.1.3)
pillar 1.8.1 2022-08-19 [2] CRAN (R 4.1.3)
pkgbuild 1.3.1 2021-12-20 [2] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.0)
pkgload 1.3.0 2022-06-27 [2] CRAN (R 4.1.3)
plotrix 3.8-2 2021-09-08 [1] CRAN (R 4.1.3)
prettyunits 1.1.1 2020-01-24 [2] CRAN (R 4.1.0)
processx 3.7.0 2022-07-07 [2] CRAN (R 4.1.3)
profvis 0.3.7 2020-11-02 [2] CRAN (R 4.1.0)
promises 1.2.0.1 2021-02-11 [2] CRAN (R 4.1.0)
ps 1.7.1 2022-06-18 [2] CRAN (R 4.1.3)
purrr 0.3.4 2020-04-17 [2] CRAN (R 4.1.0)
quadprog 1.5-8 2019-11-20 [2] CRAN (R 4.1.0)
R6 2.5.1 2021-08-19 [2] CRAN (R 4.1.1)
Rcpp 1.0.9 2022-07-08 [2] CRAN (R 4.1.3)
readxl * 1.4.2 2023-02-09 [1] CRAN (R 4.1.3)
remotes 2.4.2 2021-11-30 [2] CRAN (R 4.1.1)
rlang 1.1.1 2023-04-28 [1] CRAN (R 4.1.3)
rprojroot 2.0.3 2022-04-02 [2] CRAN (R 4.1.3)
rstudioapi 0.14 2022-08-22 [2] CRAN (R 4.1.3)
scatterplot3d 0.3-44 2023-05-05 [1] CRAN (R 4.1.3)
sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.1.1)
shiny 1.7.2 2022-07-19 [2] CRAN (R 4.1.3)
stringi 1.7.8 2022-07-11 [2] CRAN (R 4.1.3)
stringr 1.4.1 2022-08-20 [2] CRAN (R 4.1.3)
sys 3.4 2020-07-23 [2] CRAN (R 4.1.0)
tibble 3.1.8 2022-07-22 [2] CRAN (R 4.1.3)
urlchecker 1.0.1 2021-11-30 [2] CRAN (R 4.1.3)
usethis 2.1.6 2022-05-25 [2] CRAN (R 4.1.3)
utf8 1.2.2 2021-07-24 [2] CRAN (R 4.1.0)
vctrs 0.4.1 2022-04-13 [2] CRAN (R 4.1.3)
vegan * 2.6-4 2022-10-11 [1] CRAN (R 4.1.3)
withr 2.5.0 2022-03-03 [2] CRAN (R 4.1.2)
xtable 1.8-4 2019-04-21 [2] CRAN (R 4.1.0)
[1] /home/jovyan/R_library
[2] /opt/conda/lib/R/libraryRight now, I am working from in my institute's jupyter server (that's why there are so many loaded packages). When I work from my Mac (Monterey 12.5.1) the error message is the same. However, when I do it from my PC (Windows 11) the error message I get is
Error: call to 'phylocom' failed with status -1073741819I can give the session info in these cases if needed, too.
I have been checking closed issues that are similar to mine and tried different solutions, checked if my newick have scientific notations (which seem to have been causing problems to other users) but I did not find a solution that worked for me.
Could be some error on my data formatting that I am not noticing?
Thank you so much in advance!
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