Error: ClusterFuture (future_lapply-1) failed to call grmall() on cluster SOCKnode What does that mean?

[DRSEI]

I am trying to integrate my seurat object but keep getting this error. is anyone know how to fix this issue

file.anchors <- FindIntegrationAnchors(object.list = ak5.list,
  anchor.features = features, reduction = "rpca")
Scaling features for provided objects
Error: ClusterFuture (future_lapply-1) failed to call grmall() on
cluster SOCKnode #1 (on ‘localhost’). The reason reported was
‘invalid connection’. Post-mortem diagnostic: The socket
connection to the worker of ClusterFuture
future (future_lapply-1) is lost or corrupted:
Connection (connection: index=3, description="NA", class="NA",
mode="NA", text="NA", opened="NA", can read="NA", can write="NA",
id=2797, raw_id="<pointer: 0x0000000000000aed>") is no longer
valid. There is currently no registered R connection with that
index 3. As an example, this may happen if
base::closeAllConnections() have been called, for instance via
base::sys.save.image() which in turn is called if the R
session (pid 8444) is forced to terminate. The total size of the
6 globals exported is 12.84 GiB. The three largest globals are
‘...future.elements_ii’ (12.84 GiB of class ‘list’),
‘anchor.features’ (125.72 KiB of class ‘character’) and
‘...future.FUN’ (5.13 KiB of class ‘function’)

[HenrikBengtsson]

Hi, thanks for reporting. Before anything else, You just won the prize for the longest subject line here on GitHub 😛 Please use a more informative subject line next time.

The underlying problem is that the main R session can no longer communicate with the parallel R worker running in the background.

The post-mortem diagnostic provided by the error message suggests that something has badly messed up the R connections, which should not happen. This was not done by the future framework, but something else. I haven't seen this reported regarding Seurat, so I doubt it is Seurat, but you can check with them. As the error message suggests, this can happen if someone/something calls base::closeAllConnections(), which is really bad, because it corrupts R to the point it most likely have to be restarted.

For future reports, here or for other R packages, please always gives as much details as possible, e.g. calls made to reproduce this and what your sessionInfo() is. Reports with only error messages, like this one, will often be closed or ignored, because there's nothing to work with.

[DRSEI]

Hello Henrik,

Thanks but this issue is very annoying. Apologize not attached the sessionInfo()

There was no error or warning in my main program, and a few days ago I've posted another issue in the Seurat repository but the author cannot find the issue satijalab/seurat#5613. This issue was similar to satijalab/seurat#1436. I even uninstalled the R studio and re-installed the newest R the problem is still there. I follow up on suggestions on #311 but I am still unable to fix it. I really need someone help to fix this issue

The commands I used :

rm(list = ls(all.names = TRUE)) #will clear all objects includes hidden objects.
gc() #free up memrory and report the memory usage.
rm()
library(Seurat)
library(SeuratWrappers)
library("future")
 plan(multisession)
options(future.globals.onReference = "error")

#dataset1
#############################################################################
setwd("D:/lymphocytes/Lung/GSE148071_NSCLC.FengyingWu2021/RDS")
Fengyingwu<- readRDS("Fengying_Wu_step1.rds")

#############################################################################
setwd("D:/lymphocytes/Lung/GSE162500_NSCLC_PAULGUEGUEN2021/RDS")
Paul_gueguen<- readRDS("Paul_Gueguen2021_step1.rds")
DimPlot(Paul_gueguen, reduction = "umap")
dev.off()

unique([email protected]$tissue)

#dataset3
#############################################################################
setwd("D:/lymphocytes/Lung/GSE176021_Lung_PD1/RDS")
justinaxcaushi1<-readRDS("Justina_X_Caushi_step1.RDS")


#dataset4
#############################################################################
setwd("D:/lymphocytes/Lung/GSE117570_NSCLC.QianqianSong2019/RDS")
QianqianSong<-readRDS("GSE117570_NSCLC.QianqianSong2019_step1.rds")
#dataset5
#############################################################################
setwd("D:/lymphocytes/Lung/GSE131907_Nayoung_Kim2021/RDS")
Nayoung_Kim<-readRDS("GSE131907.seurat_step1.rds")
#dataset6
#############################################################################
setwd("D:/lymphocytes/Lung/lung_teichmann/RDS")
teichmann<-readRDS("lung_ts_ammended_122022.rds")

######### merging Datasets: Method 2 #######################################

ak5 <- merge(Fengyingwu, y = c(Paul_gueguen, QianqianSong,teichmann,Nayoung_Kim,justinaxcaushi1), 
             add.cell.ids = c("Feng", "Paul", "Qianqi","teichman","Nayoung","justina"), project = "Lung_integration")
ak5

# split the dataset into a list of two seurat objects 
ak5.list <- SplitObject(ak5, split.by = "tissue")
# normalizing data sets
for (i in 1:length(ak5.list)) {
  ak5.list[[i]] <- NormalizeData(ak5.list[[i]], verbose = FALSE)
  ak5.list[[i]] <- FindVariableFeatures(ak5.list[[i]], selection.method = "vst", 
                                           nfeatures = 2000, verbose = T)
}


# select features that are repeatedly variable across datasets for integration run PCA on each
# dataset using these features
features <- SelectIntegrationFeatures(object.list = ak5.list)
ak5.list <- lapply(X = ak5.list, FUN = function(x) {
  x <- ScaleData(x, features = features, verbose = FALSE)
  x <- RunPCA(x, features = features, verbose = FALSE)
})

immune.anchors <- FindIntegrationAnchors(object.list = ak5.list, anchor.features = features, reduction = "rpca")

Scaling features for provided objects
Error: ClusterFuture (future_lapply-1) failed to call grmall() on cluster SOCKnode #1 (on ‘localhost’). The reason reported was
‘invalid connection’. Post-mortem diagnostic: The socket connection to the worker of ClusterFuture
future (future_lapply-1) is lost or corrupted: Connection (connection: index=3, description="NA", class="NA",mode="NA", text="NA", opened="NA", can read="NA", can write="NA",
id=2797, raw_id="<pointer: 0x0000000000000aed>") is no longer valid. There is currently no registered R connection with that index 3. As an example, this may happen if
base::closeAllConnections() have been called, for instance via base::sys.save.image() which in turn is called if the R session (pid 8444) is forced to terminate. The total size of the 6 globals exported is 12.84 GiB. The three largest globals are
‘...future.elements_ii’ (12.84 GiB of class ‘list’), ‘anchor.features’ (125.72 KiB of class ‘character’) and
‘...future.FUN’ (5.13 KiB of class ‘function’)


> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252    
system code page: 65001

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

other attached packages:
[1] SeuratObject_4.0.4 Seurat_4.1.0      

loaded via a namespace (and not attached):
  [1] nlme_3.1-153          matrixStats_0.61.0    spatstat.sparse_2.1-0 RcppAnnoy_0.0.19      RColorBrewer_1.1-2   
  [6] httr_1.4.2            sctransform_0.3.3     tools_4.1.2           utf8_1.2.2            R6_2.5.1             
 [11] irlba_2.3.5           rpart_4.1-15          KernSmooth_2.23-20    uwot_0.1.11           mgcv_1.8-38          
 [16] lazyeval_0.2.2        colorspace_2.0-2      tidyselect_1.1.1      gridExtra_2.3         compiler_4.1.2       
 [21] cli_3.1.1             plotly_4.10.0         labeling_0.4.2        scales_1.1.1          lmtest_0.9-39        
 [26] spatstat.data_2.1-2   ggridges_0.5.3        pbapply_1.5-0         goftest_1.2-3         stringr_1.4.0        
 [31] digest_0.6.29         spatstat.utils_2.3-0  pkgconfig_2.0.3       htmltools_0.5.2       parallelly_1.30.0    
 [36] fastmap_1.1.0         htmlwidgets_1.5.4     rlang_1.0.1           shiny_1.7.1           farver_2.1.0         
 [41] generics_0.1.2        zoo_1.8-9             jsonlite_1.7.3        ica_1.0-2             dplyr_1.0.8          
 [46] magrittr_2.0.2        patchwork_1.1.1       Matrix_1.3-4          Rcpp_1.0.8            munsell_0.5.0        
 [51] fansi_1.0.2           abind_1.4-5           reticulate_1.24       lifecycle_1.0.1       stringi_1.7.6        
 [56] MASS_7.3-54           Rtsne_0.15            plyr_1.8.6            grid_4.1.2            parallel_4.1.2       
 [61] listenv_0.8.0         promises_1.2.0.1      ggrepel_0.9.1         crayon_1.4.2          miniUI_0.1.1.1       
 [66] deldir_1.0-6          lattice_0.20-45       cowplot_1.1.1         splines_4.1.2         tensor_1.5           
 [71] pillar_1.7.0          igraph_1.2.11         spatstat.geom_2.3-1   future.apply_1.8.1    reshape2_1.4.4       
 [76] codetools_0.2-18      leiden_0.3.9          glue_1.6.1            data.table_1.14.2     png_0.1-7            
 [81] vctrs_0.3.8           httpuv_1.6.5          gtable_0.3.0          RANN_2.6.1            purrr_0.3.4          
 [86] spatstat.core_2.3-2   polyclip_1.10-0       tidyr_1.2.0           scattermore_0.7       future_1.23.0        
 [91] ggplot2_3.3.5         mime_0.12             xtable_1.8-4          later_1.3.0           survival_3.2-13      
 [96] viridisLite_0.4.0     tibble_3.1.6          cluster_2.1.2         globals_0.14.0        fitdistrplus_1.1-6   
[101] ellipsis_0.3.2        ROCR_1.0-11  

[HenrikBengtsson]

Okay, thanks. Let's make sure you can run:

library(future)
plan(multisession, workers = 2)
futureSessionInfo()

in a clean R session. Does that work for you and what's the output?

[DRSEI]

Sure please see the output below

> library(future)
> plan(multisession, workers = 2)
> futureSessionInfo()
*** Package versions
future 1.23.0, parallelly 1.30.0, parallel 4.1.2, globals 0.14.0, listenv 0.8.0

*** Allocations
availableCores():
system 
     6 
availableWorkers():
$system
[1] "localhost" "localhost" "localhost" "localhost" "localhost" "localhost"

*** Settings
- future.plan=<no set>
- future.fork.multithreading.enable=<no set>
- future.globals.maxSize=<no set>
- future.globals.onReference=<no set>
- future.resolve.recursive=<no set>
- future.rng.onMisuse=<no set>
- future.wait.timeout=<no set>
- future.wait.interval=<no set>
- future.wait.alpha=<no set>
- future.startup.script=<no set>

*** Backends
Number of workers: 2List of future strategies:
1. multisession:
   - args: function (..., envir = parent.frame(), workers = 2)
   - tweaked: TRUE
   - call: plan(multisession, workers = 2)
*** Basic tests
  worker   pid     r sysname release     version        nodename machine login  user effective_user
1      1  4944 4.1.2 Windows  10 x64 build 19044 DESKTOP-KL59KU3  x86-64 elmap elmap          elmap
2      2 10508 4.1.2 Windows  10 x64 build 19044 DESKTOP-KL59KU3  x86-64 elmap elmap          elmap
Number of unique PIDs: 2 (as expected)
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