Parallel package for windows 10 in R - r

Question

I have this dataset that I'm trying to parse in R. The data from HMDB and the dataset name is Serum Metabolites (in a format of xml file). The xml file contains about 25K metabolites nodes, each I want to parse to sub-nodes
I have a code that parses the XML file to a list object in R.
Since the XML file is quite big and since for each metabolite there are about 12 sub-nodes I want, It takes a long time to parse the file. about 3 hours to 1,000 metabolites.
I'm trying to use the package parallel but receive and error.
The packages:
library("XML")
library("xml2")
library( "magrittr" ) #for pipe operator %>%
library("pbapply") # to track on progress
library("parallel")
The function:
# The function receives an XML file (its location) and returns a list of nodes
Short_Parser_HMDB <- function(xml.file_location){
start.time<- Sys.time()
# Read as xml file
doc <- read_xml( xml.file_location )
#get metabolite nodes (only first three used in this sample)
met.nodes <- xml_find_all( doc, ".//d1:metabolite" ) [1:1000] # [(i*1000+1):(1000*i+1000)] # [1:3]
#list of data.frame
xpath_child.v <- c( "./d1:accession",
"./d1:name" ,
"./d1:description",
"./d1:synonyms/d1:synonym" ,
"./d1:chemical_formula" ,
"./d1:smiles" ,
"./d1:inchikey" ,
"./d1:biological_properties/d1:pathways/d1:pathway/d1:name" ,
"./d1:diseases/d1:disease/d1:name" ,
"./d1:diseases/d1:disease/d1:references",
"./d1:kegg_id" ,
"./d1:meta_cyc_id"
)
child.names.v <- c( "accession",
"name" ,
"description" ,
"synonyms" ,
"chemical_formula" ,
"smiles" ,
"inchikey" ,
"pathways_names" ,
"diseases_name",
"references",
"kegg_id" ,
"meta_cyc_id"
)
#first, loop over the met.nodes
L.sec_acc <- parLapply(cl, met.nodes, function(x) { # pblapply to track progress or lapply but slows down dramticlly the function and parLapply fo parallel
#second, loop over the xpath desired child-nodes
temp <- parLapply(cl, xpath_child.v, function(y) {
xml_find_all(x, y ) %>% xml_text(trim = T) %>% data.frame( value = .)
})
#set their names
names(temp) = child.names.v
return(temp)
})
end.time<- Sys.time()
total.time<- end.time-start.time
print(total.time)
return(L.sec_acc )
}
Now create the enviroment :
# select the location where the XML file is
location= "D:/path/to/file//HMDB/DataSets/serum_metabolites/serum_metabolites.xml"
cl <-makeCluster(detectCores(), type="PSOCK")
clusterExport(cl, c("Short_Parser_HMDB", "cl"))
clusterEvalQ(cl,{library("parallel")
library("magrittr")
library("XML")
library("xml2")
})
And execute :
Short_outp<-Short_Parser_HMDB(location)
stopCluster(cl)
The error received:
> Short_outp<-Short_Parser_HMDB(location)
Error in checkForRemoteErrors(val) :
one node produced an error: invalid connection
base on those links, Tried to implement the parallel :
Parallel Processing in R
How to call global function from the parLapply function?
Error in R parallel:Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: cannot open the connection
but couldn't find invalid connection as an error
I'm using windows 10 the latest R version 4.0.2 (not sure if it's enough information)
Any hint or idea will be appreciated