Why I cannot get this string in RStudio? - r

Question

I am trying to read a phylogeny (as text) into R using RStudio. I copied the text and put them in quotes. But now I cannot even assign it to a variable in R.
tree = "(((((((((((((Potentilla_intermedia:0.311566,Potentilla_recta:0.311566):0.802855,Potentilla_pensylvanica:1.114421):0.041676,(Potentilla_gracilis:1.110417,Potentilla_argentea:1.110417):0.04568):8.56704,(((Potentilla_norvegica:0.063773,Potentilla_supina:0.063773):0.051902,Potentilla_hippiana:0.115675):8.590754,Argentina_anserina:8.706429):1.016709):0.602701,Potentilla_bipinnatifida:10.325839):8.923901,(((Potentilla_anglica:1.366781,Potentilla_reptans:1.366781):5.302408,(Potentilla_simplex:0.031597,Potentilla_canadensis:0.031597):6.637592):0.621378,Duchesnea_indica:7.290567):11.959172):1.543066,Potentilla_sterilis:20.792806):11.333216,(((((Fragaria_chiloensis:2.648747,Fragaria_vesca:2.648747):1.022985,Fragaria_virginiana:3.671731):17.684618,(Dasiphora_fruticosa:11.647099,Potentilla_arguta:11.647099):9.709251):0.676268,Drymocallis_arguta:22.032617):0.405466,((Alchemilla_monticola:16.875311,Alchemilla_xanthochlora:16.875311):0.887368,Comarum_palustre:17.762679):4.675404):9.687939):6.026567,((((((((Rosa_setigera:3.378155,Rosa_blanda:3.378155):0.030747,Rosa_carolina:3.408902):0.025377,Rosa_arkansana:3.434279):1.991106,((Rosa_rubiginosa:2.358272,Rosa_spinosissima:2.358272):0.07664,Rosa_multiflora:2.434911):2.990474):0.128884,Rosa_woodsii:5.554269):0.86504,Rosa_acicularis:6.419309):6.730804,(((((Rosa_micrantha:0.188519,Rosa_canina:0.188519):0.012649,Rosa_tomentosa:0.201168):0.03073,Rubus_plicatifolius:0.231898):0.29401,Rosa_palustris:0.525908):2.38304,Rosa_rugosa:2.908948):10.241165):23.677485,((((Agrimonia_pubescens:0.020923,Agrimonia_gryposepala:0.020923):3.336778,Agrimonia_striata:3.357701):1.373162,(Agrimonia_rostellata:1.363567,Agrimonia_parviflora:1.363567):3.367296):20.869366,Sanguisorba_minor:25.600229):11.227369):1.324992):6.47604,((((Geum_laciniatum:1.819705,Geum_canadense:1.819705):3.890036,(Geum_aleppicum:5.612049,Geum_urbanum:5.612049):0.097692):2.792243,((Geum_macrophyllum:2.602326,Geum_triflorum:2.602326):2.49947,Geum_vernum:5.101796):3.400188):2.651319,Geum_rivale:11.153303):33.475326):1.449852,((((((((((((((((((((((Rubus_semisetosus:2.411266,Rubus_frondosus:2.411266):0.563329,Rubus_wisconsinensis:2.974595):0.095095,(Rubus_wheeleri:2.378801,Rubus_fulleri:2.378801):0.690888):0.0356,Rubus_glandicaulis:3.10529):0.272207,(Rubus_miscix:2.288585,Rubus_spectatus:2.288585):1.088911):0.685377,(Rubus_ithacanus:3.983737,Rubus_steelei:3.983737):0.079136):0.015284,Rubus_enslenii:4.078157):0.068184,Rubus_pensilvanicus:4.146341):0.314926,(Rubus_argutus:0.58418,Rubus_cuneifolius:0.58418):3.877087):0.02081,(((Rubus_regionalis:4.019817,Rubus_canadensis:4.019817):0.059086,Rubus_rosa:4.078903):0.160428,Rubus_recurvans:4.239331):0.242746):0.015005,(Rubus_allegheniensis:4.31499,Rubus_uvidus:4.31499):0.182092):0.019612,Rubus_vermontanus:4.516694):0.891371,(Rubus_hispidus:4.440803,Rubus_permixtus:4.440803):0.967262):1.32483,Rubus_vagus:6.732895):0.023439,Rubus_superioris:6.756333):0.020104,(((((((Rubus_trivialis:1.652243,Rubus_flagellaris:1.652243):0.36229,(Rubus_multifer:0.538518,Rubus_curtipes:0.538518):1.476014):0.807236,Rubus_stipulatus:2.821768):0.295305,Rubus_junceus:3.117074):0.198123,Rubus_missouricus:3.315197):0.971918,Rubus_elegantulus:4.287115):2.388002,Rubus_alumnus:6.675117):0.101321):0.025475,((Rubus_laciniatus:0.125186,Rubus_bifrons:0.125186):0.11903,Rubus_praecox:0.244216):6.557697):4.346196,Rubus_pubescens:11.148109):0.061953,Rubus_idaeus:11.210062):0.042458,((Rubus_phoenicolasius:11.083887,Rubus_occidentalis:11.083887):0.087068,Rubus_arcticus:11.170956):0.081565):7.121242,((Rubus_uniformis:8.388795,Rubus_parviflorus:8.388795):6.470355,Rubus_odoratus:14.85915):3.514612):14.711986,Rubus_meracus:33.085749):12.992732):16.915234,((Filipendula_rubra:19.826137,Filipendula_vulgaris:19.826137):0.073841,Filipendula_ulmaria:19.899978):43.093736):13.354116,(((((((((((((((((((((((((((((((((((Crataegus_dodgei:0.015733,Crataegus_dissona:0.015733):0.010796,Crataegus_michauxii:0.026529):0.010633,Crataegus_formosa:0.037162):0.011471,Crataegus_pedicellata:0.048633):0.014098,Crataegus_irrasa:0.062731):0.019132,Crataegus_florifera:0.081863):0.032863,Crataegus_lumaria:0.114726):0.465517,Crataegus_fulleriana:0.580243):0.006081,Crataegus_disperma:0.586324):0.099168,(Crataegus_jesupii:0.549784,Crataegus_lucorum:0.549784):0.135708):0.00584,Crataegus_fluviatilis:0.691331):0.380201,Crataegus_scabrida:1.071532):0.019968,Crataegus_calpodendron:1.0915):0.033869,Crataegus_succulenta:1.125369):0.262341,((Crataegus_holmesiana:0.712472,Crataegus_mollis:0.712472):0.144634,Crataegus_coccinioides:0.857106):0.530604):0.398534,Crataegus_marshallii:1.786245):0.228259,Crataegus_crus-galli:2.014503):0.161619,Crataegus_intricata:2.176122):0.016118,((Crataegus_macrosperma:0.790887,Crataegus_pruinosa:0.790887):0.122301,(Crataegus_chrysocarpa:0.193226,Crataegus_macracantha:0.193226):0.719962):1.279051):0.017649,Crataegus_submollis:2.209889):0.014998,Crataegus_phaenopyrum:2.224886):0.018512,Crataegus_uniflora:2.243399):0.438351,Crataegus_persimilis:2.68175):0.045017,Crataegus_punctata:2.726768):0.058153,Crataegus_laevigata:2.78492):0.065678,Crataegus_spathulata:2.850598):0.26874,Crataegus_viridis:3.119338):0.332928,Crataegus_douglasii:3.452267):0.094595,Crataegus_monogyna:3.546862):3.832148,((((((Malus_toringo:2.491744,Malus_pumila:2.491744):1.007309,Malus_baccata:3.499053):1.351718,Malus_coronaria:4.850771):1.621923,(Malus_angustifolia:0.049008,Malus_ioensis:0.049008):6.423685):0.035427,Cotoneaster_divaricatus:6.50812):0.736585,Chaenomeles_speciosa:7.244705):0.134305):1.72489,((Aronia_arbutifolia:0.094396,Aronia_melanocarpa:0.094396):8.89729,(Pyrus_communis:7.94625,Sorbus_aucuparia:7.94625):1.045436):0.112214):0.313393,((((Amelanchier_spicata:5.295684,Amelanchier_sanguinea:5.295684):0.053588,Amelanchier_alnifolia:5.349272):2.667629,((Amelanchier_arborea:0.249044,Amelanchier_bartramiana:0.249044):0.767662,Amelanchier_canadensis:1.016706):7.000194):0.24348,(Amelanchier_interior:7.807145,Amelanchier_laevis:7.807145):0.453236):1.156912):0.239145,Sorbus_decora:9.656438):1.019952,Sorbus_americana:10.67639):38.78046,((((((((((((Prunus_hortulana:3.586661,Prunus_persica:3.586661):0.523019,Prunus_mexicana:4.10968):0.275607,Prunus_munsoniana:4.385286):0.329537,(Prunus_armeniaca:1.156849,Prunus_tomentosa:1.156849):3.557974):0.032697,(Prunus_angustifolia:4.478999,Prunus_pumila:4.478999):0.268521):0.03745,Prunus_alleghaniensis:4.784971):1.404974,(Prunus_americana:2.365429,Prunus_nigra:2.365429):3.824516):0.37487,(Prunus_cerasus:2.734566,Prunus_pensylvanica:2.734566):3.830249):4.856241,((Prunus_padus:1.415647,Prunus_virginiana:1.415647):3.401352,Prunus_serotina:4.817):6.604057):29.162527,Sorbaria_sorbifolia:40.583584):2.924475,(Rhodotypos_scandens:36.33611,Physocarpus_opulifolius:36.33611):7.17195):2.718224,(((Spiraea_X_bumalda:10.834237,Spiraea_alba:10.834237):3.799914,Spiraea_tomentosa:14.634152):11.287431,Aruncus_dioicus:25.921583):20.304701):3.230567):26.89098);"
Note: it works on macOS R app, but not on terminal R or RStudio.
Can anyone run the above code? I am surprised that this does not work. There must be something basic about R that I am not know, even after using it for year...
Thanks!
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.3 assertthat_0.2.1 cli_1.1.0 tools_3.5.3 withr_2.1.2 rstudioapi_0.9.0
[7] crayon_1.3.4 packrat_0.5.0 sessioninfo_1.1.1

Answer 1

I can't explain why it works differently in different console environments, and particularly why it does work in the MacOS R application (for me it doesn't work under an ESS shell in Ubuntu), but the link given above points to a comment in the Introduction to R:
Command lines entered at the console are limited^4 to about 4095 bytes (not characters)
If you put the code above in a file and source() it, it works fine. nchar(tree) is 6936.
The discussion in the link also points to the place where the limit is hardcoded in R, so if you were really desperate you could modify that value and recompile R ...