emmanuelparadis / ape

analysis of phylogenetics and evolution
http://ape-package.ird.fr/
GNU General Public License v2.0
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Bug in ape 5.5 #9

Closed TJrogers86 closed 3 years ago

TJrogers86 commented 3 years ago

SIr/Ma'am,

I have updated to the new version of ape and found a significant problem. I was able to replicate this problem on another computer as well. Any time I go to use the read.tree() function, I get the following error: Error in FUN(X[[i]], ...) : attempt to set index 746/746 in SET_STRING_ELT

This does not happen with the previous version of ape.

emmanuelparadis commented 3 years ago

Hi, Do you have a reproducible example? Maybe it comes from your data.

TJrogers86 commented 3 years ago

I tried to attach the tree file, but was unable to. So I pasted it below. Also, I was able to revert back to the prior version of ape and everything works fine. So, not sure what the issue is. The new package didnt work with this tree on mine or another college's compter.

((((((((((((((((((Pygathrix_cinerea_ott786,(Pygathrix_nemaeus_nemaeus_ott118860)Pygathrix_nemaeus_ott721486),'Pygathrix cinerea 1 RL-2012 ott266464',Pygathrix_nigripes_ott473243,'Pygathrix cinerea 2 RL-2012 ott1072539')Pygathrix_ott721485,((Simias_concolor_ott621138)Simias_ott752305,(Nasalis_larvatus_ott860954)Nasalis_ott235536)),((Rhinopithecus_bieti_ott77080,(Rhinopithecus_roxellana_ott77083,Rhinopithecus_avunculus_ott514757)),'Rhinopithecus bieti 2 RL-2012 ott945338',Rhinopithecus_brelichi_ott1068677,Rhinopithecus_strykeri_ott1072533,'Rhinopithecus bieti 1 RL-2012 ott1072537')Rhinopithecus_ott508298),(((((Trachypithecus_obscurus_ott43798,Trachypithecus_barbei_ott597818),(Trachypithecus_phayrei_phayrei_ott157188,Trachypithecus_phayrei_crepuscula_ott157189,Trachypithecus_phayrei_shanicus_ott683655,Trachypithecus_phayrei_holotephreus_ott844492)Trachypithecus_phayrei_ott703784),((Trachypithecus_germaini_ott597815,Trachypithecus_cristatus_ott735418),(Trachypithecus_auratus_auratus_ott627778,Trachypithecus_auratus_pyrrhus_ott975088,Trachypithecus_auratus_mauritius_ott1031585)Trachypithecus_auratus_ott240209)),(((Trachypithecus_delacouri_ott48788,((Trachypithecus_poliocephalus_leucocephalus_ott278062,Trachypithecus_poliocephalus_poliocephalus_ott844491)Trachypithecus_poliocephalus_ott250658,(Trachypithecus_francoisi_francoisi_ott627777)Trachypithecus_francoisi_ott43805)),Trachypithecus_hatinhensis_ott1038626),Trachypithecus_laotum_ott250663,Trachypithecus_ebenus_ott3607628)),(((Trachypithecus_geei_ott118937,Trachypithecus_pileatus_ott118938,Trachypithecus_shortridgei_ott514267),(Trachypithecus_johnii_ott514751,(Semnopithecus_priam_ott627774,(Semnopithecus_hector_ott737534,(Semnopithecus_entellus_entellus_ott1038629)Semnopithecus_entellus_ott276589),Semnopithecus_ajax_ott3607622,Semnopithecus_hypoleucos_ott3607623,Semnopithecus_schistaceus_ott3607625,Semnopithecus_natunae_ott7655048,Semnopithecus_nestor_ott7655049,Semnopithecus_palaeindicus_ott7655050,Semnopithecus_subanus_ott7655051,Semnopithecus_subhimalayanus_ott7655052)Semnopithecus_ott547162)),(Trachypithecus_vetulus_vetulus_ott834804)Trachypithecus_vetulus_ott721477),Trachypithecus_mauritius_ott6145137,Trachypithecus_selangorensis_ott6145139)),((((((Presbytis_rubicunda_rubicunda_ott36154)Presbytis_rubicunda_ott512403,Presbytis_melalophos_bicolor_ott704361),Presbytis_melalophos_sumatranus_ott704355),(Presbytis_melalophos_mitrata_ott627775,(Presbytis_comata_comata_ott627776,Presbytis_comata_fredericae_ott1032604)Presbytis_comata_ott68893),Presbytis_melalophos_melalophos_ott704360),(Presbytis_potenziani_potenziani_ott455456,Presbytis_potenziani_siberu_ott512416)Presbytis_potenziani_ott704401),(((Presbytis_chrysomelas_ott471028,Presbytis_frontata_ott704371),(Presbytis_hosei_hosei_ott704363)Presbytis_hosei_ott704364),(Presbytis_thomasi_ott512437,(Presbytis_femoralis_femoralis_ott5925581)Presbytis_femoralis_ott68891)),Presbytis_senex_ott1091914,(Presbytis_siamensis_ott3607626,Presbytis_natunae_ott3607627),Presbytis_canicrus_ott6145130,Presbytis_sabana_ott6145132,Presbytis_albigena_ott7655038,Presbytis_ignita_ott7655039,Presbytis_nobilis_ott7655040,Presbytis_pileata_ott7655041,Presbytis_robinsoni_ott7655042,Presbytis_vetulus_ott7655043)Presbytis_ott989398),(((((Colobus_guereza_matschiei_ott24727,Colobus_guereza_caudatus_ott24728,Colobus_guereza_occidentalis_ott24730,Colobus_guereza_kikuyuensis_ott664571)Colobus_guereza_ott565569,(Colobus_vellerosus_ott39815,Colobus_polykomos_ott989400)),(Colobus_angolensis_palliatus_ott713997)Colobus_angolensis_ott721482),(Colobus_satanas_satanas_ott189817)Colobus_satanas_ott189815)'Colobus (genus in Deuterostomia) ott1000283',((Procolobus_verus_ott24731)Procolobus_ott640560,((((Piliocolobus_pennantii_ott437216,Piliocolobus_preussi_ott437219),Piliocolobus_tholloni_ott1013942),((Piliocolobus_foai_ott1013930,(Piliocolobus_tephrosceles_ott1013938,Piliocolobus_rufomitratus_ott1013945)),(Piliocolobus_kirkii_ott1013935,Piliocolobus_gordonorum_ott1013949))),(Piliocolobus_badius_temminckii_ott941793,Piliocolobus_badius_badius_ott941798)Piliocolobus_badius_ott640572,Piliocolobus_bouvieri_ott6145121,Piliocolobus_epieni_ott6145122,Piliocolobus_oustaleti_ott6145123,Piliocolobus_parmentieri_ott6145124,Piliocolobus_semlikiensis_ott6145125,Piliocolobus_waldronae_ott6145127,Piliocolobus_lulindicus_ott7655037)Piliocolobus_ott1013952)))Colobinae_ott741061,((Semnopithecus_monspessulanus_ott3607642,Mesopithecus_pentelicus_ott3607661)Mesopithecus_ott3607643,(Dolichopithecus_ruscinensis_ott3607645)Dolichopithecus_ott3607633)),((((((((((Cercopithecus_ascanius_ascanius_ott5512,Cercopithecus_ascanius_schmidti_ott5513,Cercopithecus_ascanius_katangae_ott5514,Cercopithecus_ascanius_whitesidei_ott5522)Cercopithecus_ascanius_ott203184,(((Cercopithecus_cephus_cephodes_ott5521,Cercopithecus_cephus_ngottoensis_ott447892,Cercopithecus_cephus_cephus_ott526949)Cercopithecus_cephus_ott268334,(Cercopithecus_sclateri_ott3607606,(Cercopithecus_erythrotis_erythrotis_ott4117775,Cercopithecus_erythrotis_camerunensis_ott4117776)Cercopithecus_erythrotis_ott623302)),(Cercopithecus_erythrogaster_erythrogaster_ott1012837,Cercopithecus_erythrogaster_pococki_ott4117757)Cercopithecus_erythrogaster_ott179316)),(Cercopithecus_petaurista_petaurista_ott526951,Cercopithecus_petaurista_buettikoferi_ott800090)Cercopithecus_petaurista_ott949841),(((Cercopithecus_albogularis_kolbi_ott311701,Cercopithecus_albogularis_monoides_ott4117767,Cercopithecus_albogularis_francescae_ott4117768,Cercopithecus_albogularis_labiatus_ott4117769,Cercopithecus_albogularis_moloneyi_ott4117770,Cercopithecus_albogularis_erythrarchus_ott4117771,Cercopithecus_albogularis_albotorquatus_ott4117772)Cercopithecus_albogularis_ott311705,(Cercopithecus_kandti_ott3607604,Cercopithecus_doggetti_ott3607605,(Cercopithecus_mitis_mitis_ott4117760,Cercopithecus_mitis_heymansi_ott4117761,Cercopithecus_mitis_boutourlinii_ott4117762,Cercopithecus_mitis_opisthostictus_ott4117763,Cercopithecus_mitis_stuhlmanni_ott4117764)Cercopithecus_mitis_ott203191)),(Cercopithecus_nictitans_martini_ott4117758,Cercopithecus_nictitans_nictitans_ott4117759)Cercopithecus_nictitans_ott203154)),((Cercopithecus_diana_ott203187,Cercopithecus_roloway_ott699219),Cercopithecus_dryas_ott3607607)),((((Cercopithecus_pogonias_grayi_ott140200,Cercopithecus_pogonias_nigripes_ott4117754,Cercopithecus_pogonias_pogonias_ott4117755,Cercopithecus_pogonias_schwarzianus_ott4117756)Cercopithecus_pogonias_ott80548,(Cercopithecus_denti_ott198616,(Cercopithecus_wolfi_wolfi_ott311699,Cercopithecus_wolfi_elegans_ott4117773,Cercopithecus_wolfi_pyrogaster_ott4117774)Cercopithecus_wolfi_ott375164)),(Cercopithecus_mona_campbelli_ott526950,Cercopithecus_mona_mona_ott949833)Cercopithecus_mona_ott918231),Cercopithecus_neglectus_ott918233)),(Cercopithecus_hamlyni_hamlyni_ott311700)Cercopithecus_hamlyni_ott268332),((((Cercopithecus_campbelli_lowei_ott11135)Cercopithecus_campbelli_ott140251,Cercopithecus_lowei_ott3607603),(Chlorocebus_cynosuros_ott250767,(((Chlorocebus_pygerythrus_pygerythrus_ott250774,Chlorocebus_pygerythrus_hilgerti_ott644387)Chlorocebus_pygerythrus_ott571323,((Chlorocebus_aethiops_vervet_ott513911,Chlorocebus_aethiops_aethiops_ott767718)Chlorocebus_aethiops_ott268337,(Chlorocebus_tantalus_budgetti_ott644385)Chlorocebus_tantalus_ott571312)),Chlorocebus_sabaeus_ott571316),Chlorocebus_djamdjamensis_ott875546,'Chlorocebus sp. TH-2013 ott875552','Chlorocebus sp. MAS-2011 ott900343','Chlorocebus sp. LDS-2018 ott7067545')Chlorocebus_ott386004),((Erythrocebus_patas_ott268326,Erythrocebus_albigenis_ott7655030,Erythrocebus_poliophaeus_ott7655031)Erythrocebus_ott268331,(Allochrocebus_solatus_ott807150,(Allochrocebus_lhoesti_ott954691,(Allochrocebus_preussi_preussi_ott4117765,Allochrocebus_preussi_insularis_ott4117766)Allochrocebus_preussi_ott283455))Allochrocebus_ott6145102)),'Cercopithecus sp. WMS-2012 ott147337',Cercopithecus_lomamiensis_ott1072609,Cercopithecus_buettikoferi_ott7655020,Cercopithecus_grayi_ott7655021,Cercopithecus_insolitus_ott7655022,Cercopithecus_leucampyx_ott7655023,Cercopithecus_ludio_ott7655024,Cercopithecus_martini_ott7655025,Cercopithecus_nicticans_ott7655026,Cercopithecus_nigripes_ott7655027,Cercopithecus_opisthostictus_ott7655028),(((Miopithecus_talapoin_talapoin_ott417277)Miopithecus_talapoin_ott975092,Miopithecus_ogouensis_ott949834)Miopithecus_ott975095,(Allenopithecus_nigroviridis_ott721471)Allenopithecus_ott721470)),((((((Cercocebus_atys_lunulatus_ott33609,Cercocebus_atys_atys_ott5860009)Cercocebus_atys_ott268349,(Cercocebus_torquatus_torquatus_ott754307)Cercocebus_torquatus_ott268353),(((Cercocebus_galeritus_ott268347,Cercocebus_sanjei_ott3607602),Cercocebus_agilis_ott363077),Cercocebus_chrysogaster_ott554545))Cercocebus_ott842861,(Mandrillus_sphinx_ott741047,Mandrillus_leucophaeus_ott741057)Mandrillus_ott741055),((((Papio_kindae_ott436611,((((Papio_cynocephalus_ibeanus_ott485691,Papio_cynocephalus_cynocephalus_ott1081949)Papio_cynocephalus_ott115471,(Papio_ursinus_ursinus_ott1013353,Papio_ursinus_griseipes_ott7067551)Papio_ursinus_ott203159),(Papio_anubis_anubis_ott554291)Papio_anubis_ott115449),(Papio_hamadryas_hamadryas_ott741051)Papio_hamadryas_ott115463),Papio_papio_ott513904,Papio_japonicus_ott6145117)Papio_ott115460,(Rungwecebus_kipunji_ott665522)Rungwecebus_ott665520),((Lophocebus_albigena_albigena_ott554544)Lophocebus_albigena_ott554556,Lophocebus_aterrimus_ott554550)Lophocebus_ott554559),(Theropithecus_gelada_ott741053,Simopithecus_oswaldi_ott3607608)Theropithecus_ott741052)),(((((((Macaca_nigra_ott111862,Macaca_tonkeana_ott407753),Macaca_nigrescens_ott169927),Macaca_hecki_ott575296),(Macaca_maura_ott169928,(Macaca_brunnescens_ott169936,Macaca_ochreata_ott575293))),((Macaca_silenus_ott111864,(Macaca_nemestrina_nemestrina_ott575290)Macaca_nemestrina_ott689656),((Macaca_leonina_ott115044,Macaca_siberu_ott311720),Macaca_pagensis_ott825636))),((((Macaca_sinica_ott115446,((Macaca_thibetana_thibetana_ott369521)Macaca_thibetana_ott111859,(Macaca_assamensis_assamensis_ott5266831)Macaca_assamensis_ott115440)),(((Macaca_radiata_radiata_ott564819)Macaca_radiata_ott837392,Macaca_leucogenys_ott6145111),Macaca_munzala_ott927559)),Macaca_arctoides_ott689665),((Macaca_fascicularis_philippinensis_ott575292,Macaca_fascicularis_fascicularis_ott4941452,Macaca_fascicularis_aureus_ott6145110)Macaca_fascicularis_ott689668,(((Macaca_fuscata_fuscata_ott689663,Macaca_fuscata_yakui_ott855332)Macaca_fuscata_ott689660,(Macaca_mulatta_lasiotus_ott5560516,Macaca_mulatta_brevicaudus_ott5860008,Macaca_mulatta_vestita_ott7067546)Macaca_mulatta_ott689650),Macaca_cyclopis_ott1067495)))),Macaca_speciosa_ott115444,Macaca_balantak_ott660441,Macaca_sylvanus_ott689645,Macaca_prisca_ott7655032)Macaca_ott268324))Cercopithecinae_ott842860),(Prohylobates_tandyi_ott3607648)Prohylobates_ott3607640)Cercopithecidae_ott842868)Cercopithecoidea_ott386194,(((((((((((((((((((Homo_sapiens_neanderthalensis_ott83926)Homo_sapiens_ott770315,Homo_heidelbergensis_ott3607676),Homo_antecessor_ott3607681),Homo_erectus_ott3607671),Homo_habilis_ott3607678),Homo_rudolfensis_ott3607673)Homo_ott770309,(Orrorin_tugenensis_ott3607732)Praeanthropus_ott3607722),((Paranthropus_boisei_ott3607689,Paranthropus_aethiopicus_ott3607718),Paranthropus_robustus_ott3607708)Paranthropus_ott3607690),(Australopithecus_ramidus_ott3607716)Ardipithecus_ott3607705),(Sahelanthropus_tchadensis_ott3607687)Sahelanthropus_ott3607688),(Pan_troglodytes_vellerosus_ott84217,Pan_troglodytes_ellioti_ott112831,(Pan_paniscus_ott158484,Pan_troglodytes_verus_ott752847),Pan_troglodytes_schweinfurthii_ott752845,Pan_troglodytes_troglodytes_ott767875)Pan_ott417957),((Gorilla_beringei_graueri_ott317556,Gorilla_beringei_beringei_ott624503)Gorilla_beringei_ott351685,(Gorilla_gorilla_gorilla_ott417953,Gorilla_gorilla_uellensis_ott620805,Gorilla_gorilla_diehli_ott835035)Gorilla_gorilla_ott417965)Gorilla_ott417969)Homininae_ott312031,(Graecopithecus_freybergi_ott3607873)Graecopithecus_ott3607813),((Dryopithecus_brancoi_ott3607876)Dryopithecus_ott3607811,(Pierolapithecus_catalaunicus_ott6145148)Pierolapithecus_ott3607691)),((((Pongo_abelii_ott770295,(Pongo_pygmaeus_pygmaeus_ott770308)Pongo_pygmaeus_ott770302,Pongo_tapanuliensis_ott7067552)Pongo_ott417949)Ponginae_ott1082538,((Dryopithecus_giganteus_ott3607692)Gigantopithecus_ott3607693,(Dryopithecus_indicus_ott4941856)Sivapithecus_ott4941855)),(Lufengpithecus_keiyuanensis_ott3607719)Lufengpithecus_ott3607684)),(Micropithecus_songhorensis_ott3607728)Kalepithecus_ott3607720),(Morotopithecus_bishopi_ott6145147)Morotopithecus_ott3607709),((((((Hylobates_lar_carpenteri_ott96938,Hylobates_lar_lar_ott96940,Hylobates_lar_entelloides_ott96941,Hylobates_lar_vestitus_ott96952)Hylobates_lar_ott995038,(((Hylobates_muelleri_abbotti_ott96939,Hylobates_muelleri_funereus_ott96947,Hylobates_muelleri_muelleri_ott96948)Hylobates_muelleri_ott995050,(Hylobates_agilis_agilis_ott96946,Hylobates_agilis_unko_ott995037)Hylobates_agilis_ott166550),(Hylobates_moloch_ott732213,Hylobates_klossii_ott995047))),Hylobates_albibarbis_ott96942,Hylobates_pileatus_ott995054)Hylobates_ott166552,((Symphalangus_syndactylus_syndactylus_ott1055751)Symphalangus_syndactylus_ott417961)Symphalangus_ott712905),(((Nomascus_concolor_jingdongensis_ott251578,Nomascus_concolor_concolor_ott671218,Nomascus_concolor_lu_ott671219,Nomascus_concolor_furvogaster_ott826059)Nomascus_concolor_ott180370,(Nomascus_gabriellae_ott847446,(Nomascus_siki_ott995043,Nomascus_leucogenys_ott1029454))),(Nomascus_nasutus_ott440190,Nomascus_hainanus_ott492226),Nomascus_annamensis_ott5852672,'Nomascus cf. leucogenys SSH-2018 ott7067556')Nomascus_ott712901),(Hoolock_leuconedys_ott574262,Hoolock_hoolock_ott1029474,Hoolock_tianxing_ott7067554)Hoolock_ott712902)Hylobatidae_ott166544),(((Kenyapithecus_wickeri_ott3607702)Kenyapithecus_ott3607703,(Sivapithecus_alpani_ott4117748)Griphopithecus_ott4117747),((Proconsul_africanus_ott3607920,(Proconsul_heseloni_ott6145293,Proconsul_nyanzae_ott6145296))Proconsul_ott3607921)Proconsulidae_ott3607918,((Dryopithecus_vancouveringi_ott4941662)Nyanzapithecus_ott4941661)Parapithecidae_ott4941653))),(Micropithecus_clarki_ott3607729)Micropithecus_ott3607696),(((Platodontopithecus_jianghuaiensis_ott3607685)Platodontopithecus_ott3607686,((Dendropithecus_orientalis_ott3607806,Dionysopithecus_shuangouensis_ott3607808)Dionysopithecus_ott3607777)Victoriapithecidae_ott3607776),((Pithecus_antiquus_ott4941634,Pliopithecus_platyodon_ott4941636)Pliopithecus_ott4941632,(Laccopithecus_robustus_ott4941644)Laccopithecus_ott4941643)),(Bramapithecus_thorpei_ott7655061)Bramapithecus_ott4117746,(Sugrivapithecus_gregoryi_ott7655094,Sugrivapithecus_salmontanus_ott7655095)Sugrivapithecus_ott4117745,(Xenopithecus_koruensis_ott7655096)Xenopithecus_ott4117738)Catarrhini_ott842867,(((((((((((Saguinus_midas_midas_ott2025)Saguinus_midas_ott532397,Saguinus_niger_ott156859),(Saguinus_martinsi_ott156862,(Saguinus_bicolor_bicolor_ott254275)Saguinus_bicolor_ott254273)),(Saguinus_geoffroyi_ott235534,Saguinus_oedipus_ott489218)),(((((Saguinus_mystax_mystax_ott429031)Saguinus_mystax_ott1015219,Saguinus_inustus_ott765147),(Saguinus_labiatus_labiatus_ott429032)Saguinus_labiatus_ott68899),(Saguinus_imperator_subgrisescens_ott809273)Saguinus_imperator_ott489221),Saguinus_leucopus_ott920962)),((Saguinus_fuscicollis_weddelli_ott146657,(Saguinus_fuscicollis_nigrifrons_ott285519,(Saguinus_fuscicollis_leucogenys_ott285526,Saguinus_fuscicollis_fuscicollis_ott548593)),Saguinus_fuscicollis_illigeri_ott285528,Saguinus_fuscicollis_lagonotus_ott809275)Saguinus_fuscicollis_ott1015238,(Saguinus_tripartitus_ott394176,((Saguinus_melanoleucus_melanoleucus_ott429030)Saguinus_melanoleucus_ott429033,((Saguinus_nigricollis_nigricollis_ott955070)Saguinus_nigricollis_ott1015216,Saguinus_graellsi_ott955071)))),Saguinus_cruzlimai_ott5852670,Saguinus_ursulus_ott6145175)Saguinus_ott1015243,(((Mico_saterei_ott172747,Mico_cf._emiliae_ott172749,(('Callithrix sp. DB-2003 ott274346',Callithrix_aurita_ott341886,(((Callithrix_penicillata_ott341908,Callithrix_jacchus_ott1015223),Callithrix_kuhlii_ott947308),Callithrix_geoffroyi_ott683989),Callithrix_flaviceps_ott3607562)Callithrix_subgenus_Callithrix_ott7067565,(((Callithrix_humilis_ott298261)Calibella_ott7067564,(Callithrix_pygmaea_ott489225,Cebuella_niveiventris_ott7655107)Cebuella_ott3607843),(((Mico_mauesi_ott341884,Mico_humeralifer_ott683993),Mico_emiliae_ott488310),(Mico_argentatus_argentatus_ott886277)Mico_argentatus_ott1015228)),Callithrix_humeralifer_ott7655105,Callithrix_pencillata_ott7655106),Mico_rondoni_ott495388,Mico_melanurus_ott1031373,Mico_chrysoleucus_ott3607561,Mico_intermedius_ott3607563,Mico_leucippe_ott3607564,Mico_marcai_ott3607565,Mico_acariensis_ott3607567,Mico_nigriceps_ott3607568,Mico_munduruku_ott7067567,Mico_melanoleucas_ott7655108),(Callimico_goeldii_ott489230)Callimico_ott489229),(Leontopithecus_chrysomelas_ott341890,(Leontopithecus_chrysopygus_ott566865,(Leontopithecus_rosalia_ott921451,Leontopithecus_caissara_ott3607559)))Leontopithecus_ott532396))Callitrichinae_ott1015234,(((((Aotus_azarae_boliviensis_ott56003,Aotus_azarae_infulatus_ott210732,Aotus_azarae_azarae_ott411832)Aotus_azarae_ott1058659,Aotus_nigriceps_ott685852),Aotus_nancymaae_ott913299),Aotus_sp._Aot1_ott116961,'Aotus sp. SHM-2010 ott210870','Aotus sp. NIM-2003 ott240208','Aotus sp. AVB-2011 ott246708',Aotus_zonalis_ott298340,Aotus_brumbacki_ott338636,(((Aotus_griseimembra_ott583084,Aotus_lemurinus_ott897634),Aotus_trivirgatus_ott791711),Aotus_vociferans_ott685855),'Aotus sp. PDE-2004 ott632025','Aotus sp. LC-2012 ott797343','Aotus sp. MAS-2011 ott900350',Aotus_jorgehernandezi_ott3607598,Aotus_miconax_ott3607601,Aotus_boliviensis_ott7655098,Aotus_rufipes_ott7655099)'Aotus (genus in Opisthokonta) ott791708')Aotidae_ott702159),((((((Saimiri_sciureus_macrodon_ott93900,Saimiri_sciureus_cassiquiarensis_ott390936,Saimiri_sciureus_albigena_ott390937,Saimiri_sciureus_sciureus_ott738574,Saimiri_sciureus_collinsi_ott923682)Saimiri_sciureus_ott842875,(Saimiri_oerstedii_oerstedii_ott737540,Saimiri_oerstedii_citrinellus_ott1021729)Saimiri_oerstedii_ott4337),Saimiri_ustus_ott455668),(Saimiri_boliviensis_boliviensis_ott326801,Saimiri_boliviensis_peruviensis_ott390933)Saimiri_boliviensis_ott977385,Saimiri_vanzolinii_ott3607558,Saimiri_cassiquiarensis_ott6145200,Saimiri_madierae_ott7655120)Saimiri_ott842872)Saimiriinae_ott1056455,((((Cebus_albifrons_ott197032,Cebus_unicolor_ott6145189),(Cebus_kaapori_ott913292,(Cebus_olivaceus_nigrivittatus_ott1031385,Cebus_olivaceus_castaneus_ott7067571)Cebus_olivaceus_ott913293)),(Cebus_capucinus_imitator_ott5925585)Cebus_capucinus_ott217252,Cebus_aequatorialis_ott6145179,Cebus_brunneus_ott6145181,Cebus_cesarae_ott6145182,Cebus_cuscinus_ott6145183,Cebus_imitator_ott6145184,Cebus_leucocephalus_ott6145185,Cebus_malitiosus_ott6145186,Cebus_versicolor_ott6145190,Cebus_yuracus_ott6145191,Cebus_abifrons_ott7655114,Cebus_fatuellus_ott7655115,Cebus_pallidus_ott7655116)Cebus_ott217260,(((Sapajus_flavius_ott299416,(Sapajus_cay_ott775268,(Sapajus_apella_apella_ott971480,Sapajus_apella_macrocephalus_ott5857441)Sapajus_apella_ott197026)),Sapajus_libidinosus_ott748283),(Sapajus_xanthosternos_ott331561,(Sapajus_nigritus_robustus_ott886281)Sapajus_nigritus_ott411831))Sapajus_ott5846387)Cebinae_ott655808)),((((Lagothrix_lugens_ott57134,((Lagothrix_poeppigii_ott57313,Lagothrix_lagotricha_ott297528),Lagothrix_cana_ott968680),Lagothrix_flavicauda_ott3607554,Lagothrix_tschudii_ott7067563)Lagothrix_ott217262,(Brachyteles_hypoxanthus_ott574171,Brachyteles_arachnoides_ott1058645)Brachyteles_ott1058665),((((Ateles_geoffroyi_frontatus_ott90800,Ateles_geoffroyi_panamensis_ott814885,Ateles_geoffroyi_vellerosus_ott814895,Ateles_geoffroyi_yucatanensis_ott814896,Ateles_geoffroyi_azuerensis_ott5857438,Ateles_geoffroyi_ornatus_ott5857439)Ateles_geoffroyi_ott791691,(Ateles_hybridus_hybridus_ott797344)Ateles_hybridus_ott645692),(Ateles_fusciceps_robustus_ott142235,Ateles_fusciceps_rufiventris_ott5857437)Ateles_fusciceps_ott791687),(Ateles_paniscus_ott217258,((Ateles_belzebuth_marginatus_ott814887,Ateles_belzebuth_chamek_ott814889)Ateles_belzebuth_ott791705,Ateles_marginatus_ott3607557)))Ateles_ott791703)Atelinae_ott81483,(((((Alouatta_guariba_clamitans_ott142239)Alouatta_guariba_ott558069,(Alouatta_belzebul_belzebul_ott558073)Alouatta_belzebul_ott1058654),(((Alouatta_seniculus_macconnelli_ott512634,Alouatta_sara_ott814670),Alouatta_seniculus_seniculus_ott558074),Alouatta_caraya_ott791697)),((Alouatta_palliata_aequatorialis_ott558065,Alouatta_palliata_palliata_ott558067,Alouatta_palliata_trabeata_ott558068,Alouatta_palliata_coibensis_ott1084511,Alouatta_palliata_mexicana_ott1084512)Alouatta_palliata_ott1012045,Alouatta_pigra_ott558066),Alouatta_stramineus_ott659847,Alouatta_juara_ott3607545,Alouatta_discolor_ott3607550,Alouatta_ululata_ott3607551,Alouatta_arctoidea_ott3607552,Alouatta_villosa_ott7655100)Alouatta_ott489216)Alouattinae_ott81488)Atelidae_ott1056467),((((Cacajao_rubicundus_ott4319,((Cacajao_ayresi_ott6557,Cacajao_hosomi_ott6559),Cacajao_melanocephalus_ott1022358),(Cacajao_calvus_rubicundus_ott7143,Cacajao_calvus_ucayalli_ott756944,Cacajao_calvus_novaesi_ott756945,Cacajao_calvus_calvus_ott810865)Cacajao_calvus_ott1058649)Cacajao_ott1058648,(Chiropotes_albinasus_ott99704,(Chiropotes_israelita_ott571889,(Chiropotes_chiropotes_sagulata_ott5857440)Chiropotes_chiropotes_ott101531),Chiropotes_utahickae_ott571892,Chiropotes_satanas_ott842864)Chiropotes_ott842863),((Pithecia_monachus_ott340054,Pithecia_irrorata_ott1058640),(Pithecia_pithecia_pithecia_ott675169)Pithecia_pithecia_ott235545,Pithecia_albicans_ott3607571,Pithecia_aequatorialis_ott3607572,Pithecia_cazuzai_ott6145208,Pithecia_chrysocephala_ott6145209,Pithecia_hirsuta_ott6145210,Pithecia_inusta_ott6145211,Pithecia_isabela_ott6145212,Pithecia_milleri_ott6145213,Pithecia_mittermeieri_ott6145214,Pithecia_napensis_ott6145215,Pithecia_pissinattii_ott6145216,Pithecia_rylandsi_ott6145217,Pithecia_vanzolinii_ott6145218)Pithecia_ott1058652)Pitheciinae_ott758742,((((Plecturocebus_cupreus_ott34118,((Plecturocebus_hoffmannsi_ott442910,Plecturocebus_moloch_ott842880),Plecturocebus_brunneus_ott645175)),(Plecturocebus_caligatus_ott210729,(Plecturocebus_donacophilus_donacophilus_ott675170)Plecturocebus_donacophilus_ott282614),Plecturocebus_stephennashi_ott3607574,Plecturocebus_pallescens_ott3607576,Plecturocebus_oenanthe_ott3607577,Plecturocebus_aureipalatii_ott3607579,Plecturocebus_modestus_ott3607580,Plecturocebus_olallae_ott3607581,Plecturocebus_cinerascens_ott3607584,Plecturocebus_bernhardi_ott3607585,Plecturocebus_baptista_ott3607589,Plecturocebus_miltoni_ott5925591,Plecturocebus_urubambensis_ott6145205,Plecturocebus_vieirai_ott6145206,Plecturocebus_grovesi_ott7067584,Plecturocebus_toppini_ott7655124)Plecturocebus_ott5925590,(((Callicebus_personatus_personatus_ott126846,Callicebus_coimbrai_ott210726),Callicebus_personatus_nigrifrons_ott126847),Callicebus_nigrifrons_ott210741,Callicebus_ornatus_ott3607575,Callicebus_discolor_ott3607578,Callicebus_melanochir_ott3607582,Callicebus_dubius_ott3607587,Callicebus_barbarabrownae_ott3607590,Callicebus_caquetensis_ott5925586,Callicebus_castaneoventris_ott7655122)Callicebus_ott842878),(Cheracebus_lugens_ott927108,Cheracebus_torquatus_ott1058663,Cheracebus_regulus_ott3607583,Cheracebus_lucifer_ott3607586,Cheracebus_medemi_ott3607588,Cheracebus_purinus_ott3607591)Cheracebus_ott5925589)Callicebinae_ott81484)Pitheciidae_ott909605)Platyrrhini_ott339033,(Aegyptopithecus_zeuxis_ott4941646)Aegyptopithecus_ott4941645)Simiiformes_ott386195,(((((Tarsius_sangirensis_ott49187,Tarsius_lariang_ott318683),(Tarsius_wallacei_ott234367,Tarsius_tarsier_ott721280)),Tarsius_dentatus_ott712758,Tarsius_pelengensis_ott3607736,Tarsius_pumilus_ott3607739,Tarsius_fuscus_ott5925595,Tarsius_tarsius_ott6145230,Tarsius_tumpara_ott6145231,Tarsius_spectrumgurskyae_ott7655127,Tarsius_supriatnai_ott7655128)Tarsius_ott339047,((Carlito_syrichta_ott339031)Carlito_ott5925594,((Cephalopachus_bancanus_bancanus_ott7067587,Cephalopachus_bancanus_borneanus_ott7067588)Cephalopachus_bancanus_ott339050)Cephalopachus_ott6145221))Tarsiidae_ott933322)Tarsiiformes_ott702151,(Propliopithecus_ankeli_ott4941650,Propliopithecus_haeckeli_ott4941651,Aeolopithecus_chirobates_ott6145291)Propliopithecus_ott4941649)Haplorrhini_ott702152,(((((((((((((Lepilemur_jamesorum_ott3428,Lepilemur_betsileo_ott3607511),Lepilemur_mustelinus_ott388426),Lepilemur_fleuretae_ott3607513),Lepilemur_wrightae_ott3607515),Lepilemur_seali_ott68773),((((Lepilemur_otto_ott28534,(Lepilemur_manasamody_ott28538,Lepilemur_edwardsi_ott148503)),Lepilemur_microdon_ott1094522),(Lepilemur_septentrionalis_ott231273,((Lepilemur_dorsalis_ott231275,(Lepilemur_mittermeieri_ott441927,(Lepilemur_sahamalazensis_ott757737,Lepilemur_ahmansonorum_ott3607514))),(Lepilemur_ankaranensis_ott414211,(Lepilemur_tymerlachsoni_ott3607517,Lepilemur_milanoii_ott3607518))))),((((Lepilemur_hubbardorum_ott112838,Lepilemur_ruficaudatus_ott230531),Lepilemur_randrianasoloi_ott848083),Lepilemur_aeeclis_ott757736),(Lepilemur_leucopus_ott274698,Lepilemur_petteri_ott3607512))),Lepilemur_mitsinjoensis_ott68775,Lepilemur_grewcockorum_ott5839498,Lepilemur_hollandorum_ott6145316,Lepilemur_scottorum_ott6145317,Lepilemur_grandidieri_ott7655180,Lepilemur_grewcocki_ott7655181,Lepilemur_sahamalaza_ott7655182,Lepilemur_wrighti_ott7655183)Lepilemur_ott388425)Lepilemuridae_ott885703,((((((((((((Microcebus_margotmarshae_ott5146,Microcebus_mamiratra_ott560998),(Microcebus_arnholdi_ott5149,Microcebus_sambiranensis_ott765356)),Microcebus_rufus_ott148500),(((Microcebus_myoxinus_ott67369,Microcebus_berthae_ott765353),Microcebus_lehilahytsara_ott415576),Microcebus_mittermeieri_ott387144),Microcebus_tanosi_ott4117710),(Microcebus_simmonsi_ott133625,(Microcebus_jollyae_ott532147,(Microcebus_gerpi_ott732719,Microcebus_marohita_ott4117712)))),Microcebus_tavaratra_ott765352),(Microcebus_macarthurii_ott20534,((Microcebus_ravelobensis_ott148505,Microcebus_bongolavensis_ott481551),Microcebus_danfossi_ott481550))),(Microcebus_murinus_ott311211,Microcebus_griseorufus_ott765339),Microcebus_lokobensis_ott481552,Microcebus_ganzhorni_ott7067589,Microcebus_boraha_ott7655173,Microcebus_manitatra_ott7655174)Microcebus_ott734824,(Mirza_coquereli_ott16910,Mirza_sp._001y03_ott480562,Mirza_zaza_ott534565)Mirza_ott947510),(Allocebus_trichotis_ott516007)Allocebus_ott516001),(Cheirogaleus_minusculus_ott311696,((Cheirogaleus_crossleyi_ott418718,Cheirogaleus_lavasoensis_ott5839495),(Cheirogaleus_major_ott589601,Cheirogaleus_medius_ott863759)),Cheirogaleus_sibreei_ott682744,Cheirogaleus_andysabini_ott6145311,Cheirogaleus_thomasi_ott6145312,Cheirogaleus_shethi_ott7655171,Cheirogaleus_smithii_ott7655172)Cheirogaleus_ott388417),(Phaner_pallescens_ott445040,Phaner_furcifer_ott836057,Phaner_parienti_ott3607529,Phaner_electromontis_ott3607530)Phaner_ott323054)Cheirogaleidae_ott885700),(((((((Avahi_unicolor_ott132960,Avahi_cleesei_ott654909),Avahi_occidentalis_ott563621),(Avahi_laniger_ott516002,((Avahi_betsileo_ott3607507,Avahi_peyrierasi_ott3607508),Avahi_meridionalis_ott3607509)),Avahi_mooreorum_ott6145313,Avahi_ramanantsoavani_ott6145314)Avahi_ott516004,(((Propithecus_tattersalli_ott311205,Propithecus_coquereli_ott402626),(((Propithecus_deckenii_deckenii_ott672751,Propithecus_deckenii_coronatus_ott729851)Propithecus_deckenii_ott729856,(Propithecus_verreauxi_verreauxi_ott729086)Propithecus_verreauxi_ott696018),Propithecus_candidus_ott1046413)),((Propithecus_edwardsi_ott571030,(Propithecus_diadema_diadema_ott847344,Propithecus_diadema_marshi_ott847345)Propithecus_diadema_ott979430),Propithecus_perrieri_ott799550))Propithecus_ott311203),((Palaeopropithecus_ingens_ott4941433,Palaeopropithecus_maximus_ott5839497)Palaeopropithecus_ott368560)Paleopropithecidae_ott5827927),(Indri_indri_ott696022)Indri_ott696021),((Hadropithecus_stenognathus_ott370488)Hadropithecus_ott370487,(Archaeolemur_majori_ott370492,Archaeolemur_edwardsi_ott370493)Archaeolemur_ott370491))Indriidae_ott1058643),(((((((Eulemur_rufus_ott22554,(Eulemur_fulvus_collaris_ott589604,Eulemur_cinereiceps_ott975685)),(Eulemur_albifrons_ott259258,Eulemur_rufifrons_ott3607541)),Eulemur_mongoz_ott696004),((Eulemur_flavifrons_ott114057,(Eulemur_macaco_macaco_ott763525)Eulemur_macaco_ott763521),Eulemur_coronatus_ott394965,Eulemur_fulvus_fulvus_ott433500)),Eulemur_fulvus_mayottensis_ott451262,Eulemur_sanfordi_ott671251,Eulemur_fulvus_albocollaris_ott671252,Eulemur_rubriventer_ott696007)Eulemur_ott394968,((((((Hapalemur_griseus_griseus_ott97009,Hapalemur_griseus_JF2002_ott372120,Hapalemur_griseus_occidentalis_ott671256,Hapalemur_griseus_alaotrensis_ott671257,Hapalemur_griseus_meridionalis_ott1094523)Hapalemur_griseus_ott789630,Hapalemur_alaotrensis_ott3607542),Hapalemur_occidentalis_ott311692),Hapalemur_aureus_ott671260)Hapalemur_ott789636,(Prolemur_simus_ott3607543)Prolemur_ott4941435),(Lemur_catta_ott913930,Lemur_lecomystax_ott7655178)Lemur_ott913932)),(((Varecia_variegata_variegata_ott114058)Varecia_variegata_ott388420,Varecia_rubra_ott462792)Varecia_ott388419,(Pachylemur_jullyi_ott5839494)Pachylemur_ott4941436))Lemuridae_ott913933),(Megaladapis_edwardsi_ott469451)Megaladapis_ott663303)Lemuriformes_ott702142,(((Daubentonia_madagascariensis_ott50727)Daubentonia_ott190075)Daubentoniidae_ott915769)Chiromyiformes_ott702144),(((((Nycticebus_pygmaeus_ott101793,((Nycticebus_javanicus_ott946857,((Nycticebus_coucang_coucang_ott946861,Nycticebus_coucang_insularis_ott7067595)Nycticebus_coucang_ott339043,Nycticebus_bengalensis_ott1049687)),Nycticebus_menagensis_ott946859),Nycticebus_bancanus_ott6145319,Nycticebus_borneanus_ott6145320,Nycticebus_kayan_ott6145321)Nycticebus_ott152021,((Loris_lydekkerianus_malabaricus_ott673365,Loris_lydekkerianus_lydekkerianus_ott5925602)Loris_lydekkerianus_ott673378,(Loris_tardigradus_nordicus_ott1049685,Loris_tardigradus_tardigradus_ott5925603)Loris_tardigradus_ott152022,Loris_lori_ott7655195,Loris_malabaricus_ott7655196)Loris_ott863754),((Arctocebus_calabarensis_ott323051,Arctocebus_aureus_ott673376)Arctocebus_ott323053,((Perodicticus_potto_ibeanus_ott323063,Perodicticus_potto_edwarsi_ott339042)Perodicticus_potto_ott339040)Perodicticus_ott339045),(Pseudopotto_martini_ott4941439)Pseudopotto_ott4941438)Lorisidae_ott863755,((((((((Galago_alleni_ott173071,Galago_gabonensis_ott323060,Sciurocheirus_makandensis_ott6145318)Sciurocheirus_ott7067591,((Otolemur_monteiri_monteiri_ott679566,Otolemur_monteiri_argentatus_ott679567)Otolemur_monteiri_ott679564,(Otolemur_crassicaudatus_ott863763,(Otolemur_garnettii_garnettii_ott945402)Otolemur_garnettii_ott885705))Otolemur_ott885711),(Galago_granti_ott323055,Galagoides_cocos_ott3607492,(Galagoides_zanzibaricus_udzungwensis_ott5925600,Galagoides_zanzibaricus_zanzibaricus_ott5925601)Galagoides_zanzibaricus_ott552575)),(Galago_matschiei_ott271531,(Galago_moholi_ott311214,(Galago_gallarum_ott552578,(Galago_senegalensis_braccatus_ott5925597,Galago_senegalensis_senegalensis_ott5925598)Galago_senegalensis_ott863751))),Galago_braccatus_ott7655187,Galago_demidoffi_ott7655188,Galago_dunni_ott7655189,Galago_minor_ott7655190),(Galagoides_demidoff_murinus_ott5925599)Galagoides_demidoff_ott653041),Galagoides_thomasi_ott202831,Galagoides_orinus_ott679563,Galagoides_rondoensis_ott3607491,Galagoides_demidoffi_ott7655192,Galagoides_kumbirensis_ott7655193,Galagoides_udzungwensis_ott7655194),(Euoticus_elegantulus_ott323064,Euoticus_pallidus_ott3607501)Euoticus_ott323066),(Wadilemur_elegans_ott4117716)Wadilemur_ott4117715,(Paragalago_cocos_ott7067593,Paragalago_zanzibaricus_ott7067594)Paragalago_ott7067592)Galagidae_ott786233),(Saharagalago_misrensis_ott4117718)Saharagalago_ott4117717)Lorisiformes_ott702145)Strepsirrhini_ott702147,(Oligopithecus_rogeri_ott6145264,Oligopithecus_savagei_ott6145265)Oligopithecus_ott3608015),(Catopithecus_browni_ott3607907)Catopithecus_ott3607908,((Djebelemur_martinezi_ott4941594)Djebelemur_ott4941593)Adapidae_ott4941560,((Notharctus_tenebrosus_ott4941696)Notharctus_ott4941695)Notharctidae_ott4941666)Primates_ott913935;

emmanuelparadis commented 3 years ago

Thanks! That's indeed a bug which I fixed in ape 5.5-1 available on GH. The problem comes from the single-quoted labels in your tree: a correction was introduced in ape 5.5 but this actually introduced this bug. See the previous discussion (which I re-opened yesterday): https://github.com/YuLab-SMU/treeio/pull/41. The simplest solution for you is to install ape 5.5-1 from GitHub.

TJrogers86 commented 3 years ago

Thanks so much! When will the update be pushed to CRAN? As it is, if someone is using install.packages('ape') it installs 5.5. Thanks again

emmanuelparadis commented 3 years ago

I don't plan to update the version on CRAN very soon: this is a minor issue since not many Newick files have single quotes. See here where I explain the process of preparing a CRAN submission. Besides, a few other minor changes have already made to ape (see here). Thanks!