Seurat: ScaleData Error: doSnowGlobals

[23sd98fg]

Hello,
I am using the Seurat alignment tool to align two samples. I could use it until recently without problems. Now, a problem appeared when I use the ScaleData function:

Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
  one node produced an error: Object '.doSnowGlobals' not found

In one forum unrelated to Seurat I found the suggestion to install doParallel but this did not help in my case. Does anybody know how can I solve this problem?

Thank you very much for your reply!
Best,
Laura

[leonfodoulian]

Hi Laura,

Can you please share your sessionInfo(), as well as the code line that led to this error?

Best,
Leon

[23sd98fg]

Hi Leon,

Thank you for your quick reply!

This is the code line:

ctrl <- ScaleData(object = ctrl, vars.to.regress = c("nUMI", "percent.mito"))

And this is the SessionInfo:

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default


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

other attached packages:
[1] dplyr_0.7.6     Seurat_2.3.3    Matrix_1.2-14   cowplot_0.9.2   ggplot2_2.2.1   devtools_1.13.6

loaded via a namespace (and not attached):
  [1] tsne_0.1-3           segmented_0.5-3.0    nlme_3.1-137         bitops_1.0-6         bit64_0.9-7          RColorBrewer_1.1-2  
  [7] prabclus_2.2-6       tools_3.5.0          backports_1.1.2      irlba_2.3.2          R6_2.2.2             rpart_4.1-13        
 [13] KernSmooth_2.23-15   Hmisc_4.1-1          lazyeval_0.2.1       colorspace_1.3-2     trimcluster_0.1-2    nnet_7.3-12         
 [19] withr_2.1.2          tidyselect_0.2.4     gridExtra_2.3        diffusionMap_1.1-0   bit_1.1-14           compiler_3.5.0      
 [25] htmlTable_1.12       hdf5r_1.0.0          labeling_0.3         diptest_0.75-7       caTools_1.17.1       scales_0.5.0        
 [31] checkmate_1.8.5      lmtest_0.9-36        DEoptimR_1.0-8       mvtnorm_1.0-8        robustbase_0.93-1    ggridges_0.5.0      
 [37] pbapply_1.3-4        dtw_1.20-1           proxy_0.4-22         stringr_1.3.1        digest_0.6.15        mixtools_1.1.0      
 [43] foreign_0.8-70       R.utils_2.6.0        base64enc_0.1-3      pkgconfig_2.0.1      htmltools_0.3.6      htmlwidgets_1.2     
 [49] rlang_0.2.1          rstudioapi_0.7       bindr_0.1.1          jsonlite_1.5         zoo_1.8-2            ica_1.0-2           
 [55] mclust_5.4.1         gtools_3.8.1         acepack_1.4.1        R.oo_1.22.0          magrittr_1.5         modeltools_0.2-21   
 [61] Formula_1.2-3        lars_1.2             Rcpp_0.12.17         munsell_0.5.0        reticulate_1.8       ape_5.1             
 [67] R.methodsS3_1.7.1    scatterplot3d_0.3-41 stringi_1.2.3        MASS_7.3-49          flexmix_2.3-14       gplots_3.0.1        
 [73] Rtsne_0.13           plyr_1.8.4           grid_3.5.0           parallel_3.5.0       gdata_2.18.0         doSNOW_1.0.16       
 [79] lattice_0.20-35      splines_3.5.0        SDMTools_1.1-221     knitr_1.20           pillar_1.2.3         igraph_1.2.1        
 [85] fpc_2.1-11           reshape2_1.4.3       codetools_0.2-15     stats4_3.5.0         glue_1.2.0           metap_0.9           
 [91] latticeExtra_0.6-28  data.table_1.11.4    png_0.1-7            foreach_1.4.4        tidyr_0.8.1          gtable_0.2.0        
 [97] RANN_2.5.1           purrr_0.2.5          kernlab_0.9-26       assertthat_0.2.0     class_7.3-14         survival_2.41-3     
[103] tibble_1.4.2         snow_0.4-2           iterators_1.0.9      memoise_1.1.0        bindrcpp_0.2.2       cluster_2.0.7-1     
[109] fitdistrplus_1.0-9   ROCR_1.0-7     

Best,
Laura

[sozep]

Hi Laura,

I've run into the same issue. Any luck working around it? Have you tried downgrading to previous versions of Seurat?

Cheers
sc

[cramirezs]

Hello,

I am having the same problem. Already, tried version 2.2.1 and everything seems fine. Any idea about what the issue could be?

Thanks,
C

[sozep]

Hi,

Not sure about Laura, but over here my issue turned out to be a weird dependency/library sourcing thing. There were some packages I was sourcing from other users' libraries; Seurat was unhappy with doSNOW and Matrix for some reason, can't figure it out.

I cleared out my entire personal R library, did a clean install of Seurat and all its dependencies, and forced .libpaths() to my own library dir. That did the trick. Make sure you have snow, doSNOW, doParallel, Matrix packages fully installed/updated/accessible.

cheers
sc

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[raqsilva]

Hi,

I have had the same issue but managed to manually change the RegressOutResid function (called by ScaleData) located at preprocessing_internal.R to use doMC instead of doSNOW. The only issue is the progress bar is not shown anymore and no support of course.

Hope this helps,
Raquel

[GSNiyl]

hi Raquel
I am having the same problem. I do not known how to change RegressOutResid function (called by ScaleData) located at preprocessing_internal.R to use doMC instead of doSNOW in library Seurat. Could you give me help?

Thanks,
Ni

[raqsilva]

Hi Ni,

I have attached new_ScaleData.txt (rename to new_ScaleData.R once downloaded), this file contains the changed version of RegressOutResid which you will use by loading this file to your environment first to be able to call the new function.
In R you just need to do something like source('path/to/file/new_ScaleData.R'), this will load the new changed version of Seurat functions to your environment. Then, call ScaleData_2 instead of ScaleData and done!

Don't forget to install and load doMC in your script.

Hope it works for you!
Raquel