[rTassel] "Error Java heap space" if the package is already install in the Rsession

[Pauline Robert]

Hi everyone,

I'm facing a real issue with rTassel to compute distance matrix as the calculation require around 3GB of memory.

I followed the installation of rJAVA and rTASSEL, definied the options to increase java head size with options(java.parameters = c("-Xmx8000m")) before to load rTASSEL and defined the startLogger.

Sometimes I'm able to run the distanceMatrix function and sometimes not.

I noticed that it's working when i deleted rTASSEL in the win library , open a r session, defined options and then install rTASSEL again.

If rTASSEL is already installed and I open a new R session then it's not working and I'm facing the following errors

(New R session)

> setwd("C:/Users/probert/Bureau/Test")

> options(java.parameters = c("-Xmx8000m"))

> library(rTASSEL)
Welcome to rTASSEL (version 0.9.26)
 • Consider starting a TASSEL log file (see ?startLogger())

> rTASSEL::startLogger(fullPath = NULL, fileName ="test")
log4j:WARN No appenders could be found for logger (net.maizegenetics.util.LoggingUtils).
log4j:WARN Please initialize the log4j system properly.

TASSEL logging file created at: C:/Users/probert/Bureau/Test

> genoPathHMP <- "C:/Users/probert/Bureau/Test/genotype.hmp.txt"
> tasGenoHMP <- rTASSEL::readGenotypeTableFromPath(path = genoPathHMP)
> tasGenoHMP
A TasselGenotypePhenotype Dataset
  Class.............. TasselGenotypePhenotype
  Taxa............... 9011
  Positions.......... 6731
  Taxa x Positions... 60653041
---
  Genotype Table..... [x]

  Phenotype Table.... [ ]

> tasDist <- distanceMatrix(tasObj = tasGenoHMP)
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :

  java.lang.OutOfMemoryError: Java heap space

I am using a PC with Intel i7- 16G RAM-  with Windows 10 Professionnel (x64)

R version 4.1.2 (2021-11-01) -- "Bird Hippie" /Platform: x86_64-w64-mingw32/x64 (64-bit) / RStudio 2022.07.1

Java version jdk-18.0.2 and jre1.8.0_341

Does anyone had also this problem, I really don't have any idea how to fix it ...

Thank you for your help !

Best,

Pauline

[Brandon Monier]

Hi Pauline,

Just some clarification - when you mention "install", do you mean re-installing the entire package (e.g. devtools::install_github("maize-genetics/rtassel")) or just loading the library into an R session (e.g. library(rTASSEL))?

[Pauline Robert]

Hi Brandon,

Each time I want to run my script, I need first to execute  "remove.packages("rTASSEL")" and then devtools::install_bitbucket(repo = "bucklerlab/rTASSEL",ref = "master",build_vignettes = FALSE,INSTALL_opts = c("--no-multiarch"))

Otherwise it is not working.

Pauline

[Brandon Monier]

Hi Pauline,

We are actively investigating this. Out of curiosity, what memory stats do you see if you run this (pardon the rJava code):

options(java.parameters = c("-Xmx8000m"))

library(rTASSEL)

library(rJava)

rJC <- J("net/maizegenetics/util/Sizeof")

rJC$printMemoryUse()

[Pauline Robert]

Hi Brandon,

Thank you for your commitment,

In the first case when rTassel was already installed , R returned this :

> rJC <- J("net/maizegenetics/util/Sizeof")
> rJC$printMemoryUse()

-------------------------------
Current Heap Size: 1 MB
Max Available Heap: 8000 MB
-------------------------------

In the second case when rTassel was removed and re-installed , R returned nothing

> rJC <- J("net/maizegenetics/util/Sizeof")
> rJC$printMemoryUse()
>

Best,

Pauline

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