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Error: Program '*/phylocom' terminated by SIGNAL (Segmentation fault) #25

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kguidonimartins opened this issue Nov 6, 2019 · 4 comments
Closed

Error: Program '*/phylocom' terminated by SIGNAL (Segmentation fault) #25

kguidonimartins opened this issue Nov 6, 2019 · 4 comments
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bug
Milestone
v0.2

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@kguidonimartins
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Hi Scott, thanks for your work on {phylocomr} and {brranching}. These packages are amazing!

I have some trouble using phylocomr::ph_bladj. Specificaly: "Segmentation fault"

I filled this issue with the data I have using. Can you help with this?

if (!require("phylocomr")) install.packages("phylocomr")
#> Loading required package: phylocomr
if (!require("brranching")) install.packages("brranching")
#> Loading required package: brranching
#> 
#> Attaching package: 'brranching'
#> The following object is masked from 'package:phylocomr':
#> 
#>     phylomatic
if (!require("ape")) install.packages("ape")
#> Loading required package: ape

ages <- read.table(
  "https://gist.githubusercontent.com/kguidonimartins/47fe769de6ba0d194157afd8e52c3bb7/raw/c436728c90fcb6df5745b05a1ed87902273cb675/ages_for_issue.txt",
  header = TRUE,
  stringsAsFactors = FALSE
)

str(ages)
#> 'data.frame':    176 obs. of  2 variables:
#>  $ V1: chr  "euphyllophyte" "seedplants" "angiosperm" "nym2ast" ...
#>  $ V2: int  400 325 179 171 165 161 147 137 127 121 ...

spp <- read.table(
  "https://gist.githubusercontent.com/kguidonimartins/47fe769de6ba0d194157afd8e52c3bb7/raw/c9eb1072c10916ae6781a5a346901d82899e6bb6/species_for_issue.txt",
  header = TRUE,
  stringsAsFactors = FALSE
)

str(spp)
#> 'data.frame':    182 obs. of  1 variable:
#>  $ spp_names: chr  "Acer campestre" "Acer negundo" "Acer pseudoplatanus" "Acer rubrum" ...

phylomatic_tree <- brranching::phylomatic(taxa = spp$spp_names, storedtree = "zanne2014", outformat = "newick")

ape::write.tree(phylomatic_tree, "phylomatic_tree")

phylomatic_tree <- ape::read.tree("phylomatic_tree")

class(phylomatic_tree)
#> [1] "phylo"

phylocomr::ph_bladj(ages = ages, phylo = phylomatic_tree)
#> Error: Program '/home/karlo/R/x86_64-pc-linux-gnu-library/3.6/phylocomr/bin//phylocom' terminated by SIGNAL (Segmentation fault)

Created on 2019-11-06 by the reprex package (v0.3.0)

Session info 
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.1 (2019-07-05)
#>  os       Ubuntu 16.04.6 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_US                       
#>  collate  en_US.UTF-8                 
#>  ctype    pt_BR.UTF-8                 
#>  tz       America/Sao_Paulo           
#>  date     2019-11-06                  
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package           * version    date       lib source        
#>  animation           2.6        2018-12-11 [1] CRAN (R 3.6.1)
#>  ape               * 5.3        2019-03-17 [1] CRAN (R 3.6.1)
#>  assertthat          0.2.1      2019-03-21 [1] CRAN (R 3.6.1)
#>  backports           1.1.5      2019-10-02 [1] CRAN (R 3.6.1)
#>  bold                0.9.0      2019-06-27 [1] CRAN (R 3.6.1)
#>  brranching        * 0.5.0      2019-07-27 [1] CRAN (R 3.6.1)
#>  callr               3.3.2      2019-09-22 [1] CRAN (R 3.6.1)
#>  cli                 1.1.0      2019-03-19 [1] CRAN (R 3.6.1)
#>  clusterGeneration   1.3.4      2015-02-18 [1] CRAN (R 3.6.1)
#>  coda                0.19-3     2019-07-05 [1] CRAN (R 3.6.1)
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#>  foreach             1.4.7      2019-07-27 [1] CRAN (R 3.6.1)
#>  fs                  1.3.1      2019-05-06 [1] CRAN (R 3.6.1)
#>  glue                1.3.1      2019-03-12 [1] CRAN (R 3.6.1)
#>  gtools              3.8.1      2018-06-26 [1] CRAN (R 3.6.1)
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#>  iterators           1.0.12     2019-07-26 [1] CRAN (R 3.6.1)
#>  jsonlite            1.6        2018-12-07 [1] CRAN (R 3.6.1)
#>  knitr               1.25       2019-09-18 [1] CRAN (R 3.6.1)
#>  lattice             0.20-38    2018-11-04 [4] CRAN (R 3.5.1)
#>  magrittr            1.5        2014-11-22 [1] CRAN (R 3.6.1)
#>  maps                3.3.0      2018-04-03 [1] CRAN (R 3.6.1)
#>  MASS                7.3-51.4   2019-04-26 [4] CRAN (R 3.6.1)
#>  Matrix              1.2-17     2019-03-22 [4] CRAN (R 3.6.1)
#>  memoise             1.1.0      2017-04-21 [1] CRAN (R 3.6.1)
#>  mnormt              1.5-5      2016-10-15 [1] CRAN (R 3.6.1)
#>  nlme                3.1-141    2019-08-01 [4] CRAN (R 3.6.1)
#>  numDeriv            2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.1)
#>  phangorn            2.5.5      2019-06-19 [1] CRAN (R 3.6.1)
#>  phylocomr         * 0.1.4      2019-07-24 [1] CRAN (R 3.6.1)
#>  phytools            0.6-99     2019-06-18 [1] CRAN (R 3.6.1)
#>  pkgbuild            1.0.6      2019-10-09 [1] CRAN (R 3.6.1)
#>  pkgconfig           2.0.3      2019-09-22 [1] CRAN (R 3.6.1)
#>  pkgload             1.0.2      2018-10-29 [1] CRAN (R 3.6.1)
#>  plotrix             3.7-6      2019-06-21 [1] CRAN (R 3.6.1)
#>  plyr                1.8.4      2016-06-08 [1] CRAN (R 3.6.1)
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#>  processx            3.4.1      2019-07-18 [1] CRAN (R 3.6.1)
#>  ps                  1.3.0      2018-12-21 [1] CRAN (R 3.6.1)
#>  quadprog            1.5-7      2019-05-06 [1] CRAN (R 3.6.1)
#>  R6                  2.4.0      2019-02-14 [1] CRAN (R 3.6.1)
#>  Rcpp                1.0.2      2019-07-25 [1] CRAN (R 3.6.1)
#>  remotes             2.1.0      2019-06-24 [1] CRAN (R 3.6.1)
#>  reshape             0.8.8      2018-10-23 [1] CRAN (R 3.6.1)
#>  reshape2            1.4.3      2017-12-11 [1] CRAN (R 3.6.1)
#>  rlang               0.4.1      2019-10-24 [1] CRAN (R 3.6.1)
#>  rmarkdown           1.16       2019-10-01 [1] CRAN (R 3.6.1)
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#>  stringr             1.4.0      2019-02-10 [1] CRAN (R 3.6.1)
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#>  taxize              0.9.9      2019-10-17 [1] CRAN (R 3.6.1)
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#>  urltools            1.7.3      2019-04-14 [1] CRAN (R 3.6.1)
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#> 
#> [1] /home/karlo/R/x86_64-pc-linux-gnu-library/3.6
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
@sckott sckott added the bug label Nov 6, 2019
@sckott sckott added this to the v0.2 milestone Nov 6, 2019
sckott added a commit that referenced this issue Nov 6, 2019
@sckott
#25 fix for bladj, lowercase name column in ages data.frame before wr…
d50bdd2 
…iting to disk

check if a root node exists in the ages file matching the phylo root node
bump packge version
@sckott
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Contributor

sckott commented Nov 6, 2019

thanks @kguidonimartins for the issue

There's a few issues

The underlying phylocom C library is not controlled by us; it doesn't error particularly well, so we don't have good error messages about what went wrong. having said that, we can try to help with things we know about:

  1. for bladj, the root node in the tree has to have a row entry in the ages file for that node. we can warn about that, but can't fix that as the user has to provide that estimate
  2. bladj is case sensitive. we can fix that for users

pushed up a change now, reinstall remotes::install_github("ropensci/phylocomr"), restart R, and try again, should warn now about the missing root node age, and then when you fix that it should work

@kguidonimartins
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Hi @sckott , many thanks for your time

I just changed the argument storedtree = "zanne2014" to storedtree = "R20120829" and that worked.

if (!require("phylocomr")) install.packages("phylocomr")
#> Loading required package: phylocomr
if (!require("brranching")) install.packages("brranching")
#> Loading required package: brranching
#> 
#> Attaching package: 'brranching'
#> The following object is masked from 'package:phylocomr':
#> 
#>     phylomatic
if (!require("ape")) install.packages("ape")
#> Loading required package: ape

ages <- read.table(
  "https://gist.githubusercontent.com/kguidonimartins/47fe769de6ba0d194157afd8e52c3bb7/raw/c436728c90fcb6df5745b05a1ed87902273cb675/ages_for_issue.txt",
  header = TRUE,
  stringsAsFactors = FALSE
)

str(ages)
#> 'data.frame':    176 obs. of  2 variables:
#>  $ V1: chr  "euphyllophyte" "seedplants" "angiosperm" "nym2ast" ...
#>  $ V2: int  400 325 179 171 165 161 147 137 127 121 ...

spp <- read.table(
  "https://gist.githubusercontent.com/kguidonimartins/47fe769de6ba0d194157afd8e52c3bb7/raw/c9eb1072c10916ae6781a5a346901d82899e6bb6/species_for_issue.txt",
  header = TRUE,
  stringsAsFactors = FALSE
)

str(spp)
#> 'data.frame':    182 obs. of  1 variable:
#>  $ spp_names: chr  "Acer campestre" "Acer negundo" "Acer pseudoplatanus" "Acer rubrum" ...

phylomatic_tree <- brranching::phylomatic(taxa = spp$spp_names, storedtree = "R20120829", outformat = "newick")
#> NOTE: 1 taxa not matched: NA/cynodon/cynodon_dactylon, ];


ape::write.tree(phylomatic_tree, "phylomatic_tree")

phylomatic_tree <- ape::read.tree("phylomatic_tree")

class(phylomatic_tree)
#> [1] "phylo"

phylocomr::ph_bladj(ages = ages, phylo = phylomatic_tree)
#> [1] "((((pinus_sylvestris:81.250000,pinus_taeda:81.250000,pinus_banksiana:81.250000,pinus_pinaster:81.250000,pinus_resinosa:81.250000,pinus_strobus:81.250000)pinus:81.250000,pseudotsuga_menziesii:162.500000,(picea_abies:81.250000,picea_mariana:81.250000)picea:81.250000)pinaceae:81.250000,juniperus_communis:243.750000)pinales:81.250000,((((((((euonymus_europaeus:113.642426,(sapium_glandulosum:81.000000,((calophyllum_longifolium:27.000000,hypericum_perforatum:27.000000):27.000000,garcinia_madruno:54.000000):27.000000,(populus_nigra:40.500000,populus_tremuloides:40.500000)populus:40.500000)malpighiales:32.642426)celastrales_to_malpighiales:32.642426,((((fagus_grandifolia:34.000000,(quercus_alba:17.000000,quercus_robur:17.000000,quercus_rubra:17.000000)quercus:17.000000)fagaceae:32.714142,(((betula_papyrifera:16.678535,betula_populifolia:16.678535,betula_alleghaniensis:16.678535,betula_pendula:16.678535)betula:16.678535,(alnus_glutinosa:16.678535,alnus_incana:16.678535):16.678535)betuloideae:16.678535,((carpinus_betulus:16.678535,carpinus_caroliniana:16.678535)carpinus:16.678535,corylus_avellana:33.357071)coryloideae:16.678535):16.678535):32.714142,((((prunus_spinosa:15.666667,prunus_virginiana:15.666667,prunus_avium:15.666667,prunus_emarginata:15.666667,prunus_serotina:15.666667)prunus:15.666667,(sorbus_aucuparia:15.666667,crataegus_monogyna:15.666667)pyrinae:15.666667):15.666667,sanguisorba_minor:47.000000,geum_urbanum:47.000000,filipendula_vulgaris:47.000000,(potentilla_argentea:23.500000,potentilla_intermedia:23.500000)potentilla:23.500000,fragaria_vesca:47.000000,rosa_canina:47.000000,rubus_idaeus:47.000000)rosaceae:29.000000,(((trema_micrantha:19.000000,urtica_dioica:19.000000):19.000000,ulmus_americana:38.000000):19.000000,rhamnus_cathartica:57.000000):19.000000)rosales:23.428284):23.428284,(((((((trifolium_dubium:8.000000,trifolium_hirtum:8.000000,trifolium_hybridum:8.000000,trifolium_incarnatum:8.000000,trifolium_pratense:8.000000,trifolium_repens:8.000000)trifolium:8.000000,lathyrus_pratensis:16.000000):8.000000,((medicago_lupulina:8.000000,medicago_minima:8.000000,medicago_polymorpha:8.000000,medicago_sativa:8.000000)medicago:8.000000,melilotus_officinalis:16.000000):8.000000):8.000000,astragalus_glycyphyllos:32.000000):8.000000,(robinia_pseudoacacia:20.000000,lotus_corniculatus:20.000000):20.000000):8.000000,ulex_europaeus:48.000000):8.000000,vicia_sativa:56.000000,cercis_canadensis:56.000000)fabaceae:66.856567):23.428284):32.642426,(((spondias_mombin:82.809090,((acer_campestre:27.603029,acer_negundo:27.603029,acer_pseudoplatanus:27.603029,acer_rubrum:27.603029,acer_saccharum:27.603029)acer:27.603029,cedrela_odorata:55.206059):27.603031):27.603027,(((alyssum_alyssoides:24.000000,(brassica_oleracea:12.000000,brassica_rapa:12.000000)brassica:12.000000,arabis_glabra:24.000000,(lepidium_campestre:12.000000,lepidium_virginicum:12.000000)lepidium:12.000000,sinapis_arvensis:24.000000,descurainia_sophia:24.000000)brassicaceae:24.103027,reseda_luteola:48.103027):24.103027,(tilia_americana:34.000000,ceiba_pentandra:34.000000)malvaceae:38.206055)malvales_to_brassicales:38.206062):38.206062,((terminalia_amazonia:88.000000,(epilobium_angustifolium:44.000000,epilobium_ciliatum:44.000000)epilobium:44.000000)myrtales:30.309090,geranium_dissectum:118.309090):30.309090)malvids:30.309097):30.309082,liquidambar_styraciflua:209.236359):30.309097,(((((((((plantago_lanceolata:45.212124,(veronica_arvensis:22.606062,veronica_beccabunga:22.606062,veronica_chamaedrys:22.606062,veronica_officinalis:22.606062,veronica_persica:22.606062)veronica:22.606062)plantaginaceae:22.606060,((spathodea_campanulata:38.000000,tabebuia_heterophylla:38.000000,tecoma_stans:38.000000,jacaranda_copaia:38.000000)bignoniaceae:14.909092,(mimulus_guttatus:39.681820,((salvia_pratensis:13.227273,thymus_vulgaris:13.227273):13.227273,prunella_vulgaris:26.454546):13.227274):13.227272):14.909092):14.909088,(fraxinus_americana:41.363636,fraxinus_excelsior:41.363636)fraxinus:41.363636):14.909096,(solanum_dulcamara:48.818184,capsicum_annuum:48.818184):48.818184):14.909088,((galium_album:35.500000,galium_aparine:35.500000,galium_mollugo:35.500000,galium_verum:35.500000)galium:35.500000,asclepias_syriaca:71.000000)gentianales:41.545456,cordia_alliodora:112.545456):41.545456,(((((sambucus_nigra:57.000000,viburnum_lantana:57.000000)adoxaceae:24.000000,symphoricarpos_albus:81.000000)dipsacales:15.181816,(heracleum_sphondylium:33.000000,daucus_carota:33.000000,foeniculum_vulgare:33.000000)apiaceae:63.181816):15.181816,(((((helianthus_annuus:22.000000,((solidago_canadensis:7.333333,conyza_canadensis:7.333333):7.333333,achillea_millefolium:14.666667):7.333333):7.333334,(leontodon_hispidus:14.666667,sonchus_oleraceus:14.666667):14.666667):7.333334,(((centaurea_scabiosa:9.166667,centaurea_solstitialis:9.166667,centaurea_jacea:9.166667)centaurea:9.166667,cirsium_arvense:18.333334):9.166666,carlina_vulgaris:27.500000):9.166668):7.333333,lactuca_serriola:44.000000,(senecio_sylvaticus:22.000000,senecio_vulgaris:22.000000)senecio:22.000000)asteraceae:46.000000,(campanula_medium:45.000000,campanula_rapunculoides:45.000000)campanula:45.000000)asterales:21.363632):21.363632,ilex_aquifolium:132.727264)campanulids:21.363647):21.363632,(anagallis_arvensis:87.727272,calluna_vulgaris:87.727272):87.727272)ericales_to_asterales:21.363632,(cornus_florida:98.409088,cornus_sanguinea:98.409088)cornus:98.409088)asterids:21.363647,(((rumex_acetosella:14.000000,rumex_crispus:14.000000,rumex_obtusifolius:14.000000,rumex_acetosa:14.000000)rumex:14.000000,persicaria_maculosa:28.000000,polygonum_aviculare:28.000000)polygonaceae:56.000000,((stellaria_media:34.333332,holosteum_umbellatum:34.333332,(cerastium_arvense:17.166666,cerastium_fontanum:17.166666,cerastium_glomeratum:17.166666,cerastium_tomentosum:17.166666)cerastium:17.166666,(silene_nutans:17.166666,silene_vulgaris:17.166666)silene:17.166666)caryophyllaceae:17.166668,(amaranthus_retroflexus:19.000000,(chenopodium_album:9.500000,chenopodium_rubrum:9.500000,chenopodium_vulvaria:9.500000)chenopodium:9.500000)amaranthaceae:32.500000):32.500000)caryophyllales:134.181824):21.363632):21.363632,(((ranunculus_acris:65.000000,helleborus_foetidus:65.000000)ranunculaceae:65.303040,berberis_vulgaris:130.303040):65.303024,papaver_rhoeas:195.606064):65.303024)eudicots:21.363617,((poa_pratensis:12.000000,(festuca_pratensis:6.000000,festuca_rubra:6.000000)festuca:6.000000,(zea_mays:9.000000,((bromus_hordeaceus:3.000000,bromus_tectorum:3.000000)bromus:3.000000,avena_barbata:6.000000):3.000000):3.000000,anthoxanthum_odoratum:12.000000,hordeum_murinum:12.000000,cynosurus_cristatus:12.000000,dactylis_glomerata:12.000000,phleum_pratense:12.000000,deschampsia_cespitosa:12.000000,alopecurus_pratensis:12.000000,arrhenatherum_elatius:12.000000,koeleria_macrantha:12.000000)poaceae:135.136353,synechanthus_warscewiczianus:147.136353)commelinids:135.136353)poales_to_asterales:21.363647,liriodendron_tulipifera:303.636353)magnoliales_to_asterales:21.363636)seedplants:1.000000;\n"
#> attr(,"ages_file")
#> [1] "/tmp/RtmpD8C8mZ/ages"
#> attr(,"phylo_file")
#> [1] "/tmp/RtmpD8C8mZ/phylo_6c90799289c1"

Created on 2019-11-11 by the reprex package (v0.3.0)

Session info 
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                       
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#> 
#> [1] /home/karlo/R/x86_64-pc-linux-gnu-library/3.6
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library

@sckott
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sckott commented Nov 11, 2019

okay, so this is solved for you now? or no?

@kguidonimartins
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kguidonimartins commented Nov 11, 2019 via email

@sckott sckott closed this as completed Nov 11, 2019
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