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

[kguidonimartins]

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

``` r 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) #> codetools 0.2-16 2018-12-24 [4] CRAN (R 3.5.2) #> combinat 0.0-8 2012-10-29 [1] CRAN (R 3.6.1) #> conditionz 0.1.0 2019-04-24 [1] CRAN (R 3.6.1) #> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1) #> crul 0.8.4 2019-08-02 [1] CRAN (R 3.6.1) #> curl 4.2 2019-09-24 [1] CRAN (R 3.6.1) #> data.table 1.12.4 2019-10-03 [1] CRAN (R 3.6.1) #> desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1) #> devtools 2.2.1 2019-09-24 [1] CRAN (R 3.6.1) #> digest 0.6.22 2019-10-21 [1] CRAN (R 3.6.1) #> ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1) #> evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.1) #> expm 0.999-4 2019-03-21 [1] CRAN (R 3.6.1) #> fastmatch 1.1-0 2017-01-28 [1] CRAN (R 3.6.1) #> 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) #> highr 0.8 2019-03-20 [1] CRAN (R 3.6.1) #> htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.1) #> httpcode 0.2.0 2016-11-14 [1] CRAN (R 3.6.1) #> igraph 1.2.4.1 2019-04-22 [1] CRAN (R 3.6.1) #> 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) #> prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1) #> 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) #> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1) #> scatterplot3d 0.3-41 2018-03-14 [1] CRAN (R 3.6.1) #> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1) #> stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.1) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1) #> sys 3.3 2019-08-21 [1] CRAN (R 3.6.1) #> taxize 0.9.9 2019-10-17 [1] CRAN (R 3.6.1) #> testthat 2.3.0 2019-11-05 [1] CRAN (R 3.6.1) #> triebeard 0.3.0 2016-08-04 [1] CRAN (R 3.6.1) #> urltools 1.7.3 2019-04-14 [1] CRAN (R 3.6.1) #> usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.1) #> uuid 0.1-2 2015-07-28 [1] CRAN (R 3.6.1) #> withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1) #> xfun 0.10 2019-10-01 [1] CRAN (R 3.6.1) #> xml2 1.2.2 2019-08-09 [1] CRAN (R 3.6.1) #> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.6.1) #> zoo 1.8-6 2019-05-28 [1] CRAN (R 3.6.1) #> #> [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]

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]

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

``` r 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 2019-11-11 #> #> ─ Packages ────────────────────────────────────────────────────────────── #> package * version date lib #> animation 2.6 2018-12-11 [1] #> ape * 5.3 2019-03-17 [1] #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.5 2019-10-02 [1] #> bold 0.9.0 2019-06-27 [1] #> brranching * 0.5.0 2019-07-27 [1] #> callr 3.3.2 2019-09-22 [1] #> cli 1.1.0 2019-03-19 [1] #> clusterGeneration 1.3.4 2015-02-18 [1] #> coda 0.19-3 2019-07-05 [1] #> codetools 0.2-16 2018-12-24 [4] #> combinat 0.0-8 2012-10-29 [1] #> conditionz 0.1.0 2019-04-24 [1] #> crayon 1.3.4 2017-09-16 [1] #> crul 0.8.4 2019-08-02 [1] #> curl 4.2 2019-09-24 [1] #> data.table 1.12.6 2019-10-18 [1] #> desc 1.2.0 2018-05-01 [1] #> devtools 2.2.1 2019-09-24 [1] #> digest 0.6.22 2019-10-21 [1] #> ellipsis 0.3.0 2019-09-20 [1] #> evaluate 0.14 2019-05-28 [1] #> expm 0.999-4 2019-03-21 [1] #> fastmatch 1.1-0 2017-01-28 [1] #> foreach 1.4.7 2019-07-27 [1] #> fs 1.3.1 2019-05-06 [1] #> glue 1.3.1 2019-03-12 [1] #> gtools 3.8.1 2018-06-26 [1] #> highr 0.8 2019-03-20 [1] #> htmltools 0.4.0 2019-10-04 [1] #> httpcode 0.2.0 2016-11-14 [1] #> igraph 1.2.4.1 2019-04-22 [1] #> iterators 1.0.12 2019-07-26 [1] #> jsonlite 1.6 2018-12-07 [1] #> knitr 1.25 2019-09-18 [1] #> lattice 0.20-38 2018-11-04 [4] #> magrittr 1.5 2014-11-22 [1] #> maps 3.3.0 2018-04-03 [1] #> MASS 7.3-51.4 2019-04-26 [4] #> Matrix 1.2-17 2019-03-22 [4] #> memoise 1.1.0 2017-04-21 [1] #> mnormt 1.5-5 2016-10-15 [1] #> nlme 3.1-142 2019-11-07 [4] #> numDeriv 2016.8-1.1 2019-06-06 [1] #> phangorn 2.5.5 2019-06-19 [1] #> phylocomr * 0.1.5.9100 2019-11-11 [1] #> phytools 0.6-99 2019-06-18 [1] #> pkgbuild 1.0.6 2019-10-09 [1] #> pkgconfig 2.0.3 2019-09-22 [1] #> pkgload 1.0.2 2018-10-29 [1] #> plotrix 3.7-6 2019-06-21 [1] #> plyr 1.8.4 2016-06-08 [1] #> prettyunits 1.0.2 2015-07-13 [1] #> processx 3.4.1 2019-07-18 [1] #> ps 1.3.0 2018-12-21 [1] #> quadprog 1.5-7 2019-05-06 [1] #> R6 2.4.0 2019-02-14 [1] #> Rcpp 1.0.2 2019-07-25 [1] #> remotes 2.1.0 2019-06-24 [1] #> reshape 0.8.8 2018-10-23 [1] #> reshape2 1.4.3 2017-12-11 [1] #> rlang 0.4.1 2019-10-24 [1] #> rmarkdown 1.16 2019-10-01 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> scatterplot3d 0.3-41 2018-03-14 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> stringi 1.4.3 2019-03-12 [1] #> stringr 1.4.0 2019-02-10 [1] #> sys 3.3 2019-08-21 [1] #> taxize 0.9.9 2019-10-17 [1] #> testthat 2.3.0 2019-11-05 [1] #> triebeard 0.3.0 2016-08-04 [1] #> urltools 1.7.3 2019-04-14 [1] #> usethis 1.5.1 2019-07-04 [1] #> uuid 0.1-2 2015-07-28 [1] #> withr 2.1.2 2018-03-15 [1] #> xfun 0.10 2019-10-01 [1] #> xml2 1.2.2 2019-08-09 [1] #> yaml 2.2.0 2018-07-25 [1] #> zoo 1.8-6 2019-05-28 [1] #> source #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.2) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> Github (ropensci/phylocomr@0533a69) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> #> [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]

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

[kguidonimartins]

Yup! Thanks

On Mon, Nov 11, 2019, 17:09 Scott Chamberlain notifications@github.com wrote:

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/phylocomr/issues/25?email_source=notifications&email_token=AB6JBVWYEON2URXUXJONJA3QTG3WFA5CNFSM4JJ3VA2KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDX63VY#issuecomment-552594903, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB6JBVVPRD2SGGIR3YSJZITQTG3WFANCNFSM4JJ3VA2A .