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Rserve.exe error: Information: Fatal error: unable to initialize the JIT, Error in glue(.Internal(R.home()), #195

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rmd13 opened this issue Oct 10, 2023 · 4 comments
Open

Rserve.exe error: Information: Fatal error: unable to initialize the JIT, Error in glue(.Internal(R.home()), #195

rmd13 opened this issue Oct 10, 2023 · 4 comments

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@rmd13
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rmd13 commented Oct 10, 2023 •
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Many years ago I installed R-3.5.1 and Rstudio on Windows8.1. To use R by other applications, I also installed the RServe and RSclient and they worked very well.

Recently for some reason I have to install R-4.3.1 to load some downloaded *.qs files (Quick Serialization of R Objects) into R workspace using package qs. These .qs file-loaded workspace have SingleCellExperiment variables which have many dependent packages that only works on R-4.3.1, that's why I installed R-4.3.1.

To access these data from other applications, I also install.package('Rserve') and install.package('RSclient') on R-4.3.1.

The problem is that although Rserve/RSclient works well inside Rstudio with R-4.3.1,it shows error when called from other applications, or directly run Rserve.exe from command line.

Scenario 1:
RSclient: 0.7.3
RServe: 1.7.3.1
I set R_HOME = C:\Program Files\R\R-3.5.1
then run C:\Users\rmd\Documents\R\win-library\3.5\Rserve\libs\x64\Rserve.exe --RS-port 6312
it opens a normal black window and works OK.

Scenario 2:
RSclient: 0.7.9
RServe: 1.8.11
I set R_HOME = C:\Program Files\R\R-4.3.1
then run C:\Users\rmd\AppData\Local\R\win-library\4.3\Rserve\libs\x64\Rserve.exe --RS-port 6312

it opens a error dialogue saying: "Information: Fatal error: unable to initialize the JIT"
The black window shows:
    Error in glue(.Internal(R.home()), "library", "base", "R", "base", sep = .Platfo
    rm$file.sep) :
      4 arguments passed to .Internal(paste) which requires 3
    Error in attach(NULL, name = "Autoloads") :
      could not find function "attach"
    Error in options(help_type = "html") : could not find function "options"
    Error: object '.ArgsEnv' not found

I have tested RSclient/RServe inside RStudio and it works well for both Scenario 1 and Scenario 2.

For example, in Scenario 2:
RSclient: 0.7.9
RServe: 1.8.11
I set R_HOME = C:\Program Files\R\R-4.3.1
RStudio select 64-bit C:\Program Files\R\R-4.3.1 then restart

 > library('Rserve')
         Warning messages:
         1: R graphics engine version 16 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. 
         2: ‘matrixStats’is build using R4.4.0
         3: In loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
           package ‘GenomeInfoDbData’ has no 'package.rds' in Meta/

  >library('RSclient')
  >Rserve(debug = FALSE, 6312) 
       Starting Rserve... 
           "C:\Users\rmd\DOCUME~1\R\WIN-LI~1\3.5\Rserve\libs\x64\Rserve.exe" --RS-port 6312 
   >c1 = RSconnect(host = "localhost", port = 6312)
   >var1 = RSeval(c1,'pp<-564535')  it add var1 into RStudio workspace with value 564535
   >var2 = RSeval(c1,'2343565')     it add var2 into RStudio workspace with value 2343565
   >RSassign(c1,123, quote('abc'))  no error
   >var_abc = RSeval(c1,quote(abc)) it add var_abc into RStudio workspace with value 123
   >RSassign(c1,456, 'def')         no error
   >var_def = RSeval(c1,quote(def)) it add var_def into RStudio workspace with value 456
   >RSassign(c1, 1:5, quote(a$foo)) 
       Error in RSassign(c1, 1:5, quote(a$foo)) : remote assign failed (This is a unstable trivial error I do not know the reason but do not care.)

What could be the possible reason for this "unable to initialize the JIT" error?
Could it because my win8.1 system is too old and damaged?( I use system recovery this year because of a virus attack, After that my Windows Update was permanently dead, my serial number was erased, and the .NET is not working (with a very old version of .NET) causing a few of my software unable to work. Win8.1 is also not supported officially now. But my laptop could still support 98%of my needs and I have to keep on it because many codes works on my laptop)
Is there a way to fix it? Or should I change the version of RServe and RSclient?
Thanks a lot.
@rmd13 rmd13 changed the title Rserve error: Information: Fatal error: unable to initialize the JIT, Error in glue(.Internal(R.home()), Rserve.exe error: Information: Fatal error: unable to initialize the JIT, Error in glue(.Internal(R.home()), Oct 10, 2023
@s-u
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s-u commented Oct 10, 2023

Howe did you start Rserve? You cannot start Rserve directly on Windows, because it doesn't use absolute paths to libraries. Instead, Windows relies on the PATH environment variable and from the above it looks like you have the old version of R on your PATH while trying to load the Rserve linked against the new version. I would strongly suggest using the Rserve::Rserve() function to start Rserve on Windows as anything else requires you to setup the correct environment by hand. Alternatively, make sure your PATH includes the correct R version first. Another alternative is to use the built-in server from R with run.Rserve().

@rmd13
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rmd13 commented Oct 11, 2023 •
edited
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Hi, I figured it out. To use Rserve with R-4.3.1, I have to update both R_HOME to C:\Program Files\R\R-4.3.1\bin\x64 and update the path environment variable's R part to C:\Program Files\R\R-4.3.1\bin\x64, then I can communicate from Matlab to R via the java binding.

One thing is that the R-4.3.1 installed Rserve and RSclient with a version of RSclient: 0.7.9 RServe: 1.8.11. I found that the two jar files:
C:\Users\rmd\AppData\Local\R\win-library\4.3\Rserve\java\REngine.jar
C:\Users\rmd\AppData\Local\R\win-library\4.3\Rserve\java\Rserve.jar
are built using Java 11, but my Matlab is Java 7 and thus cannot load these two jars, thus cannot connect to the successfully established Rserve window.

To make it, I went to the official website
https://www.rforge.net/Rserve/snapshot/Rserve_1.8-12.tar.gz
and click downloaded the top two jars (They are luckily build in Java7, but I cannot figure out the version of the Rserve they are fitted with):

, and place them inside this folder (delete the two existing jars of java 11.).
C:\Users\rmd\AppData\Local\R\win-library\4.3\Rserve\java\REngine.jar
C:\Users\rmd\AppData\Local\R\win-library\4.3\Rserve\java\RserveEngine.jar

Although the name differs for RserveEngine.jar vs Rserve.jar, I can load these two jars into MATLAB and communicate with the established Rserve:

c = org.rosuda.REngine.Rserve.RConnection('127.0.0.1',aPort);
x = c.eval('R.version.string');
disp(x.asString());

c.eval('library(''RCurl'')'); %ok
c.eval('library(RCurl)');%ok
c.eval('a<-4566');%ok
aa = c.eval('a')
aa.asDouble %4566

% load a qs file into Rserve and get data into matlab:
c.eval('library(''qs'')');
c.eval('a2 <- qread(''D:\QMDownload\9\annotations_Astro_Final_anno.qs'')');
a = c.eval('a2');%org.rosuda.REngine.REXPGenericVector@7ef2d7a6+[25]named
aAs = a.asNativeJavaObject;
...

@rmd13
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rmd13 commented Oct 11, 2023 •
edited
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I load one qs file which is a R vector and get the data into matlab as a REXPGenericVector.

c.eval('a2 <- qread(''D:\QMDownload\9\annotations_Astro_Final_anno.qs'')');
a = c.eval('a2');%org.rosuda.REngine.REXPGenericVector@7ef2d7a6+[25]named

The following fields are true for this data from all the is* fields.

a.isList            
a.isRecursive
a.isVector

Then I load another qs file which is a very complicated SingleCellExperiment variable that only after I installed many dependent packages I can load this data into the Rstudio working space severe days before.

Now I am facing a problem that this complicated data although transferred to matlab, its type is REXPS4.
I tried all the is*, but all of them are false. The .asNativeJavaObject method also shows error:

Java exception occurred:
org.rosuda.REngine.REXPMismatchException: attempt to access
org.rosuda.REngine.REXPS4 as native Java Object

	at org.rosuda.REngine.REXP.asNativeJavaObject(REXP.java:85)

Why the SingleCellExperiment variable cannot be further analyzed in matlab? Is there a possible way?
Thanks.

Update: the toDebugString prints many useful data inside, but they are incomplete because the real data is much longer. They are printed in a chaos manner. I cannot get them organized.

a3.toDebugString

Update 2:
ss = javaMethod('_attr',a3) %org.rosuda.REngine.REXPList@121c54fa[10]named
% looks interesting, I will dig further
ss2 = ss.asList;
% great, it works!
for i = 0: ss2.capacity-1
ss3 = ss2.elementAt(i);
ss4 = ss3.asNativeJavaObject;
...

end

ans =
<org.rosuda.REngine.REXPList@121c54fa[10]{int_metadata=<org.rosuda.REngine.REXPList@4390f46e[1]{names=org.rosuda.REngine.REXPString@7c6442c2[3]{"version","spike_names","size_factor_names"}}>org.rosuda.REngine.REXPGenericVector@2d746ce4[3]{<org.rosuda.REngine.REXPList@5dbf5634[1]{class=org.rosuda.REngine.REXPString@1948ea69[2]{"package_version","numeric_version"}}>org.rosuda.REngine.REXPGenericVector@47e4d9d0[1]{org.rosuda.REngine.REXPInteger@49798e84[3]{1,12,0}},
org.rosuda.REngine.REXPString@6ed06f69[0]{},
org.rosuda.REngine.REXPString@3015db78[0]{}},
int_elementMetadata=<org.rosuda.REngine.REXPList@515ebef3[7]{rownames=org.rosuda.REngine.REXPSymbol@545607f2[�NULL�],
nrows=org.rosuda.REngine.REXPInteger@39109136[1]{32111},
listData=<org.rosuda.REngine.REXPList@27c04377[1]{names=org.rosuda.REngine.REXPString@34dc85a[1]{"rowPairs"}}>org.rosuda.REngine.REXPGenericVector@67403656[1]{<org.rosuda.REngine.REXPList@5a6482a9[7]{rownames=org.rosuda.REngine.REXPSymbol@7f9ab969[�NULL�],
nrows=org.rosuda.REngine.REXPInteger@12f8b1d8[1]{32111},
listData=<org.rosuda.REngine.REXPList@746cd757[1]{names=org.rosuda.REngine.REXPString@ae372b9[0]{}}>org.rosuda.REngine.REXPGenericVector@2098d37d[0]{},
elementType=org.rosuda.REngine.REXPString@77b9d0c7[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@65fd6708[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@749ab7b4[0]{},
class=<org.rosuda.REngine.REXPList@127f9161[1]{package=org.rosuda.REngine.REXPString@2bf94401[1]{"S4Vectors"}}>org.rosuda.REngine.REXPString@2532b351[1]{"DFrame"}}>org.rosuda.REngine.REXPS4@4349754},
elementType=org.rosuda.REngine.REXPString@6a2eea2a[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@b967222[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@3b0ee03a[0]{},
class=<org.rosuda.REngine.REXPList@1ba05e38[1]{package=org.rosuda.REngine.REXPString@6c298dc[1]{"S4Vectors"}}>org.rosuda.REngine.REXPString@3e7dfd44[1]{"DFrame"}}>org.rosuda.REngine.REXPS4@723ed581,
int_colData=<org.rosuda.REngine.REXPList@6b760460[7]{rownames=org.rosuda.REngine.REXPSymbol@796065aa[�NULL�],
nrows=org.rosuda.REngine.REXPInteger@28a6301f[1]{1191},
listData=<org.rosuda.REngine.REXPList@2c306a57[1]{names=org.rosuda.REngine.REXPString@773e2eb5[3]{"reducedDims","altExps","colPairs"}}>org.rosuda.REngine.REXPGenericVector@d8948cd[3]{<org.rosuda.REngine.REXPList@1436a7ab[7]{rownames=org.rosuda.REngine.REXPSymbol@3b7b05a8[�NULL�],
nrows=org.rosuda.REngine.REXPInteger@3d36dff4[1]{1191},
listData=<org.rosuda.REngine.REXPList@7abe27bf[1]{names=org.rosuda.REngine.REXPString@5b94ccbc[0]{}}>org.rosuda.REngine.REXPGenericVector@38a1c423[0]{},
elementType=org.rosuda.REngine.REXPString@336365bc[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@38eb2fb0[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@4567e53d[0]{},
class=<org.rosuda.REngine.REXPList@7351a16e[1]{package=org.rosuda.REngine.REXPString@5bb7643d[1]{"S4Vectors"}}>org.rosuda.REngine.REXPString@3ac04654[1]{"DFrame"}}>org.rosuda.REngine.REXPS4@4074023c,
<org.rosuda.REngine.REXPList@3ed0918d[7]{rownames=org.rosuda.REngine.REXPSymbol@5e268ce6[�NULL�],
nrows=org.rosuda.REngine.REXPInteger@66ec9390[1]{1191},
listData=<org.rosuda.REngine.REXPList@6e91893[1]{names=org.rosuda.REngine.REXPString@3c0fbd3a[0]{}}>org.rosuda.REngine.REXPGenericVector@562457e1[0]{},
elementType=org.rosuda.REngine.REXPString@54562ea6[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@1a35993f[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@5b12012e[0]{},
class=<org.rosuda.REngine.REXPList@2f7dcef2[1]{package=org.rosuda.REngine.REXPString@4a3be6a5[1]{"S4Vectors"}}>org.rosuda.REngine.REXPString@7cf162bc[1]{"DFrame"}}>org.rosuda.REngine.REXPS4@3721177d,
<org.rosuda.REngine.REXPList@766a4535[7]{rownames=org.rosuda.REngine.REXPSymbol@63718b93[�NULL�],
nrows=org.rosuda.REngine.REXPInteger@14e2e1c3[1]{1191},
listData=<org.rosuda.REngine.REXPList@2b4786dd[1]{names=org.rosuda.REngine.REXPString@f202d6d[0]{}}>org.rosuda.REngine.REXPGenericVector@60e21209[0]{},
elementType=org.rosuda.REngine.REXPString@630d1b2f[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@746b18fd[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@7a2e0858[0]{},
class=<org.rosuda.REngine.REXPList@aac3f4e[1]{package=org.rosuda.REngine.REXPString@1f38957[1]{"S4Vectors"}}>org.rosuda.REngine.REXPString@2df3c564[1]{"DFrame"}}>org.rosuda.REngine.REXPS4@2715644a},
elementType=org.rosuda.REngine.REXPString@4c2869a9[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@518cf84a[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@62e7dffa[0]{},
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rowRanges=<org.rosuda.REngine.REXPList@35835fa[6]{unlistData=<org.rosuda.REngine.REXPList@56f71edb[8]{seqnames=<org.rosuda.REngine.REXPList@7207cb51[5]{values=<org.rosuda.REngine.REXPList@2a27cb34[2]{levels=org.rosuda.REngine.REXPString@6892cc6f[0]{},
class=org.rosuda.REngine.REXPString@6fd1660[1]{"factor"}}>org.rosuda.REngine.REXPFactor@4a6c18ad[0]{},
lengths=org.rosuda.REngine.REXPInteger@5e8604bf[0]{},
elementMetadata=org.rosuda.REngine.REXPSymbol@20095ab4[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@4e2916c3[0]{},
class=<org.rosuda.REngine.REXPList@64aad6db[1]{package=org.rosuda.REngine.REXPString@ae7950d[1]{"S4Vectors"}}>org.rosuda.REngine.REXPString@60d1b21f[1]{"Rle"}}>org.rosuda.REngine.REXPS4@66c83fc8,
strand=<org.rosuda.REngine.REXPList@546621c4[5]{values=<org.rosuda.REngine.REXPList@621f89b8[2]{levels=org.rosuda.REngine.REXPString@f339eae[3]{"+","-","*"},
class=org.rosuda.REngine.REXPString@2822c6ff[1]{"factor"}}>org.rosuda.REngine.REXPFactor@4dafba3e[0]{},
lengths=org.rosuda.REngine.REXPInteger@53e3a87a[0]{},
elementMetadata=org.rosuda.REngine.REXPSymbol@40368a46[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@7e9da981[0]{},
class=<org.rosuda.REngine.REXPList@4ed38226[1]{package=org.rosuda.REngine.REXPString@3d43fe[1]{"S4Vectors"}}>org.rosuda.REngine.REXPString@74ad8d05[1]{"Rle"}}>org.rosuda.REngine.REXPS4@676ff3b0,
ranges=<org.rosuda.REngine.REXPList@35ff8fc9[7]{start=org.rosuda.REngine.REXPInteger@5fb7183b[0]{},
width=org.rosuda.REngine.REXPInteger@476a736d[0]{},
NAMES=org.rosuda.REngine.REXPSymbol@5f80fa43[�NULL�],
elementType=org.rosuda.REngine.REXPString@16c8b7bd[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@7159139f[�NULL�],
metadata=org.rosuda.REngine.REXPGenericVector@65bcf7c2[0]{},
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seqinfo=<org.rosuda.REngine.REXPList@5a8ba37c[5]{seqnames=org.rosuda.REngine.REXPString@37c2eacb[0]{},
seqlengths=org.rosuda.REngine.REXPInteger@232cce0[0]{},
is_circular=org.rosuda.REngine.REXPLogical@32b9bd12[0]{},
genome=org.rosuda.REngine.REXPString@352e787a[0]{},
class=<org.rosuda.REngine.REXPList@159a48a6[1]{package=org.rosuda.REngine.REXPString@15bc339[1]{"GenomeInfoDb"}}>org.rosuda.REngine.REXPString@7e75bf2d[1]{"Seqinfo"}}>org.rosuda.REngine.REXPS4@385ef531,
elementMetadata=<org.rosuda.REngine.REXPList@7fc645e4[7]{rownames=org.rosuda.REngine.REXPSymbol@205b132e[�NULL�],
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elementType=org.rosuda.REngine.REXPString@58112bc4[1]{"ANY"},
elementMetadata=org.rosuda.REngine.REXPSymbol@2301b75[�NULL�],
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elementType=org.rosuda.REngine.REXPString@258ee7de[1]{"ANY"},
metadata=org.rosuda.REngine.REXPGenericVector@4930539b[0]{},
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elementMetadata=<org.rosuda.REngine.REXPList@6e1d4137[7]{rownames=org.rosuda.REngine.REXPSymbol@256a1825[�NULL�],
nrows=org.rosuda.REngine.REXPInteger@29a4f594[1]{32111},
listData=<org.rosuda.REngine.REXPList@57b75756[1]{names=org.rosuda.REngine.REXPString@5327a06e[23]{"ensembl_gene_id","anno_seqnames","anno_start","anno_end","anno_width","anno_strand","gene_id","gene_name","gene_biotype","seq_coord_system","symbol","entrezid","gene_short_name","ID","QC_ssGenes","QC_g2mGenes","QC_mtGenes","QC_IEG_Genes","QC_medianExp","QC_top50_expressed","QC_meanExp","QC_detectionRate","QC_varExp"}}>org.rosuda.REngine.REXPGenericVector@2679311f[23]{org.rosuda.REngine.REXPString@287f7811[32111]{"ENSG00000121410","ENSG00000268895","ENSG00000148584","ENSG00000175899","ENSG00000245105","ENSG00000166535","ENSG00000256661","ENSG00000256904","ENSG00000184389","ENSG00000128274","ENSG00000094914","ENSG00000081760","ENSG00000197953","ENSG00000188984","ENSG00000109576","ENSG00000158122","ENSG00000103591","ENSG00000115977","ENSG00000087884","ENSG00000127837","ENSG00000129673","ENSG00000131043","ENSG00000205002","ENSG00000090861","ENSG00000124608","ENSG00000266967","ENSG00000157426","ENSG00000149313","ENSG00000008311","ENSG00000276072","ENSG00000181409","ENSG00000225180",..},
<org.rosuda.REngine.REXPList@451f87af[2]{levels=org.rosuda.REngine.REXPString@2b556bb2[357]{"1","10","11","12","13","14","15","16","17","18","19","2","20","21","22","3","4","5","6","7","8","9","CHR_HG107_PATCH","CHR_HG126_PATCH","CHR_HG1311_PATCH","CHR_HG1342_HG2282_PATCH","CHR_HG1362_PATCH","CHR_HG142_HG150_NOVEL_TEST","CHR_HG151_NOVEL_TEST","CHR_HG1651_PATCH","CHR_HG1832_PATCH","CHR_HG2021_PATCH",..},
class=org.rosuda.REngine.REXPString@44cb460e[1]{"factor"}}>org.rosuda.REngine.REXPFactor@17271176[32111]{11,11,2,4,4,4,4,4,1,15,4,4,16,1,17,22,7,12,3,12,9,13,21,8,19,9,17,3,20,126,9,9,..},
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>>

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s-u commented Oct 12, 2023

You won't be able to handle S4 objects in matlab, you have to use S4 methods in R to extract what you need from those obejcts or convert them to regular types (like matrices, vectors etc.). Of course, you could manually dig into it the internal structure, but that is highly discouraged, because only the methods know the internal structure, users should never see it and it may change at any point.

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