Cluster setup fail - germination cleanup code for R

[mmjulkowska]

Hi - happy Wednesday!

Thanks for developing this software. I am trying to run the Germination assay. Preprocessing of the images went great in ImageJ, and I have the project on in R-studio, but when I run the R code for cleanup_germination_data - I get the following error.

Error in makePSOCKcluster(names = spec, ...) : 
  Cluster setup failed. 7 of 7 workers failed to connect.

Do you know what could be causing the issue? I am attaching my sessionInfo() below:

R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rlang_0.4.10      RcppRoll_0.3.0    zoo_1.8-8         data.table_1.12.8 doParallel_1.0.16 iterators_1.0.12  foreach_1.5.0    
[8] dplyr_1.0.0       pacman_0.5.1     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6     rstudioapi_0.11  magrittr_1.5     tidyselect_1.1.0 lattice_0.20-41  R6_2.4.1         tools_4.0.0     
 [8] grid_4.0.0       packrat_0.5.0    ellipsis_0.3.1   tibble_3.0.1     lifecycle_0.2.0  crayon_1.3.4     purrr_0.3.4     
[15] vctrs_0.3.0      codetools_0.2-16 glue_1.4.1       compiler_4.0.0   pillar_1.4.4     generics_0.0.2   pkgconfig_2.0.3

[jonasoh]

Hi, and a merry Wednesday to you too!

I have a hunch that it may be related to this bug in R. Could you please try running it on R 4.1.2?

[mmjulkowska]

working well now - thanks!

[jonasoh]

Great! I'll add it to the troubleshooting table.