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

[RASpicer]

I've just updated ggtree on 2 MacBooks which have different OS and R versions but am getting the same error when trying to run ggtree on both:

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

The first laptop is running macOS Catalina 10.15.7, with R 4.0.5.

> library(ggtree)
> tree <- rtree(50)
> ggtree(tree)
Error in DataMask$new(.data, caller_env) : 
  argument "caller_env" is missing, with no default
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggtree_2.4.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6          magrittr_2.0.1      tidyselect_1.1.1    aplot_0.0.6         munsell_0.5.0      
 [6] colorspace_2.0-1    ape_5.5             lattice_0.20-44     R6_2.5.0            rlang_0.4.11       
[11] fansi_0.4.2         dplyr_1.0.6         patchwork_1.1.1     tools_4.0.5         parallel_4.0.5     
[16] grid_4.0.5          gtable_0.3.0        nlme_3.1-152        utf8_1.2.1          DBI_1.1.1          
[21] ellipsis_0.3.2      lazyeval_0.2.2      assertthat_0.2.1    tibble_3.1.1        lifecycle_1.0.0    
[26] crayon_1.4.1        treeio_1.14.4       tidyr_1.1.3         BiocManager_1.30.15 purrr_0.3.4        
[31] ggplot2_3.3.3       vctrs_0.3.8         tidytree_0.3.3      glue_1.4.2          compiler_4.0.5     
[36] pillar_1.6.0        rvcheck_0.1.8       generics_0.1.0      scales_1.1.1        jsonlite_1.7.2     
[41] pkgconfig_2.0.3    

The second laptop is running macOS Big Sur 11.3.1 with R 4.0.3.

> library(ggtree)
> tree <- rtree(50)
> ggtree(tree)
Error in DataMask$new(.data, caller_env) : 
  argument "caller_env" is missing, with no default
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggnewscale_0.4.5   shinyWidgets_0.6.0 shinythemes_1.2.0  ggtree_2.4.2      
[5] ape_5.5            forcats_0.5.1      stringr_1.4.0      dplyr_1.0.6       
[9] purrr_0.3.4        readr_1.4.0        tidyr_1.1.3        tibble_3.1.1      
[13] ggplot2_3.3.3      tidyverse_1.3.1    shiny_1.6.0       

loaded via a namespace (and not attached):
[1] Rcpp_1.0.6          lubridate_1.7.10    lattice_0.20-44     assertthat_0.2.1   
[5] digest_0.6.27       utf8_1.2.1          mime_0.10           R6_2.5.0           
[9] cellranger_1.1.0    backports_1.2.1     reprex_2.0.0        httr_1.4.2         
[13] pillar_1.6.0        rlang_0.4.11        lazyeval_0.2.2      readxl_1.3.1       
[17] rstudioapi_0.13     jquerylib_0.1.4     munsell_0.5.0       broom_0.7.6        
[21] compiler_4.0.3      httpuv_1.6.1        modelr_0.1.8        pkgconfig_2.0.3    
[25] htmltools_0.5.1.1   tidyselect_1.1.1    fansi_0.4.2         crayon_1.4.1       
[29] dbplyr_2.1.1        withr_2.4.2         later_1.2.0         grid_4.0.3         
[33] nlme_3.1-152        jsonlite_1.7.2      xtable_1.8-4        gtable_0.3.0       
[37] lifecycle_1.0.0     DBI_1.1.1           magrittr_2.0.1      scales_1.1.1       
[41] cachem_1.0.4        tidytree_0.3.3      cli_2.5.0           stringi_1.5.3      
[45] fs_1.5.0            promises_1.2.0.1    bslib_0.2.4         xml2_1.3.2         
[49] ellipsis_0.3.2      rvcheck_0.1.8       generics_0.1.0      vctrs_0.3.8        
[53] treeio_1.14.4       tools_4.0.3         glue_1.4.2          hms_1.0.0          
[57] parallel_4.0.3      fastmap_1.1.0       colorspace_2.0-1    BiocManager_1.30.15
[61] aplot_0.0.6         rvest_1.0.0         haven_2.4.1         sass_0.3.1         
[65] patchwork_1.1.1

[GuangchuangYu]

see also #395. pls re-install ggtree from source code.

[blacksoilwan]

the problem still exist

remotes::install_github("YuLab-SMU/ggtree", force = TRUE)
Downloading GitHub repo YuLab-SMU/ggtree@HEAD
Running R CMD build...

• checking for file ‘/private/var/folders/6v/8gm5bnb919561hrmf3dx_0y00000gn/T/RtmpwOYJUX/remotes12f505b93438b/YuLab-SMU-ggtree-384cc42/DESCRIPTION’ ... OK
• preparing ‘ggtree’:
• checking DESCRIPTION meta-information ... OK
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building ‘ggtree_2.99.0.tar.gz’
• installing source package ‘ggtree’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
• DONE (ggtree)

library(ggplot2)
library(ggtree)
p1<-read.csv("heatmap1.csv", header = TRUE, row.names = 1)
p1.clust<-hclust(dist(p1))
p2<-ggtree(p1.clust)
Error in DataMask$new(.data, caller_env) :
argument "caller_env" is missing, with no default

[jrherr]

Along with this issue and the next one, I'm getting this same error out of the blue on two separate MacOS systems.

I've now reinstalled ggtree and dplyr and a fresh R install and I am still getting the same error:

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

Just here so I can get a ping when there is a fix. Thanks!

[alexkrohn]

Echoing this sentiment. Same problems here running R 4.0.5 and Mojave 10.14.6, with all ggtree dependencies up to date.

[pbreslin1]

Same issue here, running the latest version of R, RevGadets 1.0.0 and ggtree 2.4.2 compiled from source code, on a PC running Windows 10.

[chrstraub]

cross-posted on other tread about the same issue.

I had the same problem with R 4.0.3 on a Mac.
used BiocManager::install("ggtree")
which requested to update dplyr to 1.0.6, which I did.

Same error message as above:
Error in DataMask$new(.data, caller_env) : argument "caller_env" is missing, with no default

also tried deinstalling ggtree, updating dplyr and reinstalling from CRAN or BiocManager - still same error.

But then I just downgraded dplyr to v1.0.5, reinstalled ggtree and that resolved the issue! So try that if you are stuck.

[pbreslin1]

Thank you, that totally worked, except I didn't have to uninstall and reinstall ggtree. I just uninstalled dplyr and installed the older version. (On Windows 10, latest version of R). Peter Breslin, PhD Environmental Life Sciences Arizona State University Biology Educator at Geffen Academy at UCLA

…

On Fri, May 14, 2021 at 9:44 PM crispina ***@***.***> wrote: cross-posted on other tread about the same issue. I had the same problem with R 4.0.3 on a Mac. used BiocManager::install("ggtree") which requested to update dplyr to 1.0.6, which I did. Same error message as above: Error in DataMask$new(.data, caller_env) : argument "caller_env" is missing, with no default also tried deinstalling ggtree, updating dplyr and reinstalling from CRAN or BiocManager - still same error. But then I just downgraded dplyr to v1.0.5, reinstalled ggtree and that resolved the issue! So try that if you are stuck. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#399 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUCP6PWBZIM7BV3FQ2A3SDDTNX32FANCNFSM44WJHHLQ> .

[gmd2020]

ISSUE RESOLVED

Solution as follows from the developer:

Please also update tidytree by remotes::install_github("YuLab-SMU/tidytree") . This is beacuse the mutate.tbl_tree in tidytree was not updated in old version.

I also rolled back dplyr from 1.0.6 to 1.0.5 as per his instructions. Not sure whether the tidytree change would have been suffcient,, and I'm not brave enough to try.

All fixed now....

REF: #400 (comment)

[gmd2020]

Thank you very much. Have rolled back to dplyr 1.0.5 and followed your suggestion regarding tidytree() All working now, very grateful… Regards Greg From: Guangchuang Yu ***@***.***> Sent: Friday, 21 May 2021 7:30 PM To: YuLab-SMU/ggtree ***@***.***> Cc: gmd2020 ***@***.***>; Comment ***@***.***> Subject: Re: [YuLab-SMU/ggtree] Error in DataMask$new(.data, caller_env) : argument "caller_env" is missing, with no default (#399) see also #400 (comment)<#400 (comment)>. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#399 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUDKCHCR2W3Q342VO5PR6CDTOYRXVANCNFSM44WJHHLQ>.

[Thu-Hang-PI]

I installed dplyr 1.0.5 as you guide. Now i can work with ggtree.
Thank you so much