ggtree() WILL NOT RUN returns error "Error in DataMask$new(.data, caller_env) : argument "caller_env" is missing, with no default"

[apostrophe D]

I run this simple code

# install the package

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("ggtree")

library(ggtree) # load the package

set.seed(2017-02-16) # load some data

tree <- rtree(50)ree # load some data

ggtree(tree)       # display a tree

This worked (once) but ever since, it returns this error:

"Error in DataMask$new(.data, caller_env) :    argument "caller_env" is missing, with no default"

Session info is reported below.  Running latest versions of R, Rstudio, etc.

Have tried re-installing R and Rstudio, running as Admin / not admin, installing as Admin/not admin, have tried rolling back dplyr version from 1.0.6 to 1.0.4 - all without success.

sessionInfo()

R version 4.0.5 (2021-03-31)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:

[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252

[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C

[5] LC_TIME=English_Australia.1252

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] devtools_2.4.1 usethis_2.0.1 ggtree_2.4.2

loaded via a namespace (and not attached):

[1] Rcpp_1.0.6 pillar_1.6.1 compiler_4.0.5 BiocManager_1.30.15 remotes_2.3.0

[6] prettyunits_1.1.1 tools_4.0.5 testthat_3.0.2 pkgload_1.2.1 pkgbuild_1.2.0

[11] aplot_0.0.6 memoise_2.0.0 jsonlite_1.7.2 tidytree_0.3.3 lifecycle_1.0.0

[16] tibble_3.1.1 nlme_3.1-152 gtable_0.3.0 lattice_0.20-41 pkgconfig_2.0.3

[21] rlang_0.4.11 cli_2.5.0 rvcheck_0.1.8 patchwork_1.1.1 parallel_4.0.5

[26] treeio_1.14.4 fastmap_1.1.0 withr_2.4.2 dplyr_1.0.6 desc_1.3.0

[31] generics_0.1.0 vctrs_0.3.8 fs_1.5.0 rprojroot_2.0.2 grid_4.0.5

[36] tidyselect_1.1.1 glue_1.4.2 R6_2.5.0 processx_3.5.2 fansi_0.4.2

[41] sessioninfo_1.1.1 callr_3.7.0 ggplot2_3.3.3 purrr_0.3.4 tidyr_1.1.3

[46] magrittr_2.0.1 ps_1.6.0 scales_1.1.1 ellipsis_0.3.2 ape_5.5

[51] colorspace_2.0-1 utf8_1.2.1 lazyeval_0.2.2 munsell_0.5.0 cachem_1.0.4

[56] crayon_1.4.1

[Davina Campbell]

I am also getting this error. I have been trying all day by changing  dplyr version from 1.0.6 to 1.0.5 and tidyverse. Also install ggtree from the source. These changes did not solve the issue.

library(ggtree)

tree <- read.tree("DendroExport.nwk")

ggtree(tree)

Error in DataMask$new(.data, caller_env) : 

  argument "caller_env" is missing, with no default

Thanks,

Davina 

[Yu, Guangchuang]

see Error in DataMask$new(.data, caller_env) : argument "caller_env" is missing, with no default · Issue #395 · YuLab-SMU/ggtree (github.com)

--
1. G Yu*. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. https://doi.org/10.1002/cpbi.96
2. LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. http://dx.doi.org/10.1093/molbev/msz240
3. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. https://doi.org/10.1093/molbev/msy194
4. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. https://doi.org/10.1111/2041-210X.12628
5. Book: https://yulab-smu.top/treedata-book/
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--

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Guangchuang Yu PhD

Professor, Director

Department of Bioinformatics
School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://yulab-smu.top

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