Possible bug in extract_tables()

[mspittler]

Hello, I experience a possible bug on MacOS BigSur with java jdk 16 in the function extract_tables(). I wasn't able to extract tables from files, which I was able to open on Linux. But for instance extract_text() works.

Error message:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  java.lang.reflect.InaccessibleObjectException: Unable to make public boolean java.util.ArrayList$Itr.hasNext() accessible: module java.base does not "opens java.util" to unnamed module @1139b2f3

Traceback:

6: stop(structure(list(message = "java.lang.reflect.InaccessibleObjectException: Unable to make public boolean java.util.ArrayList$Itr.hasNext() accessible: module java.base does not \"opens java.util\" to unnamed module @1139b2f3", 
       call = .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", 
           cl, .jcast(if (inherits(o, "jobjRef") || inherits(o, 
               "jarrayRef")) o else cl, "java/lang/Object"), .jnew("java/lang/String", 
               method), j_p, j_pc, use.true.class = TRUE, evalString = simplify, 
           evalArray = FALSE), jobj = new("jobjRef", jobj = <pointer: 0x7ff6e5e1a0c0>, 
           jclass = "java/lang/reflect/InaccessibleObjectException")), class = c("InaccessibleObjectException", 
   "RuntimeException", "Exception", "Throwable", "Object", "error", 
   "condition")))
5: .jcheck(silent = FALSE)
4: .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, 
       .jcast(if (inherits(o, "jobjRef") || inherits(o, "jarrayRef")) o else cl, 
           "java/lang/Object"), .jnew("java/lang/String", method), 
       j_p, j_pc, use.true.class = TRUE, evalString = simplify, 
       evalArray = FALSE)
3: .jrcall(x, name, ...)
2: guessesIterator$hasNext()
1: tabulizer::extract_tables(pdf)

sessionInfo()

R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] tabulizer_0.2.2

loaded via a namespace (and not attached):
 [1] tabulizerjars_1.0.1 httr_1.4.2          compiler_4.0.4      magrittr_2.0.1      R6_2.5.0            tools_4.0.4         curl_4.3            yaml_2.2.1         
 [9] xml2_1.3.2          rvest_1.0.0         lifecycle_1.0.0     rlang_0.4.10        rJava_0.9-13        png_0.1-7 

[Arf9999]

I'm having the same issue.

[kzarada]

I am having the same issue but on a windows. The other tabulizer functions work fine but extract_table throws an error when using the sample code:

library("tabulizer")
f <- system.file("examples", "data.pdf", package = "tabulizer")
tab <- extract_tables(f, pages = 1)

The error is: Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : java.lang.reflect.InaccessibleObjectException: Unable to make public boolean java.util.ArrayList$Itr.hasNext() accessible: module java.base does not "opens java.util" to unnamed module @327514f

[ivoggv]

I'm having the same issue with extract_tables. Here is the output. Does someone has an answer? Thanks in advance.

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : java.lang.reflect.InaccessibleObjectException: Unable to make public boolean java.util.ArrayList$Itr.hasNext() accessible: module java.base does not "opens java.util" to unnamed module @a530d0a

[matthewstern]

Exact same issue here! Running 64bit R, JRE 1.8.0_291 and JDK 16.0.1 on Windows. New to tabulizer, would love to get it working, but likewise extract_table throws the identical error posted by @kzarada @ivoggv, etc. extract_text works. For what it's worth this StackExchange answer seems to refer to this problem pretty clearly, but I don't know enough (Read: anything) about Java so don't know what to do with the answer.

[Sheksta]

I have this issue too! Running jdk-16.0.2, R 4.0.5.

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  java.lang.reflect.InaccessibleObjectException: Unable to make public boolean java.util.ArrayList$Itr.hasNext() accessible: module java.base does not "opens java.util" to unnamed module @41e36e46

>sessionInfo()

R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
[1] tabulizer_0.2.2

loaded via a namespace (and not attached):
[1] tabulizerjars_1.0.1 compiler_4.0.4      tools_4.0.4         rJava_1.0-4         png_0.1-7 

[swsoyee]

Same here.

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  java.lang.reflect.InaccessibleObjectException: Unable to make public boolean java.util.ArrayList$Itr.hasNext() accessible: module java.base does not "opens java.util" to unnamed module @4ba534b0

> sessionInfo()
R version 4.1.1 Patched (2021-09-01 r80852)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] tabulizer_0.2.2   data.table_1.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7          magrittr_2.0.1      xtable_1.8-4        R6_2.5.1            rlang_0.4.11       
 [6] fastmap_1.1.0       stringr_1.4.0       tools_4.1.1         shiny.i18n_0.2.0    png_0.1-7          
[11] htmltools_0.5.2     ellipsis_0.3.2      yaml_2.2.1          digest_0.6.27       lifecycle_1.0.0    
[16] rJava_1.0-4         shiny_1.6.0         later_1.3.0         promises_1.2.0.1    glue_1.4.2         
[21] mime_0.11           stringi_1.7.4       compiler_4.1.1      tabulizerjars_1.0.1 jsonlite_1.7.2     
[26] httpuv_1.6.2 

~ java --version
openjdk 17 2021-09-14
OpenJDK Runtime Environment Homebrew (build 17+0)
OpenJDK 64-Bit Server VM Homebrew (build 17+0, mixed mode)

 ~ javac -version
javac 17

[swsoyee]

Thanks for the relate thread which is provided by @matthewstern, I found a way how to avoid this error, just downgrade your jdk to 1.8, which is JAVA8 not JAVA 9 or later.

And here is my new session info and Java version:

 ~ java -version
openjdk version "1.8.0_292"
OpenJDK Runtime Environment (AdoptOpenJDK)(build 1.8.0_292-b10)
OpenJDK 64-Bit Server VM (AdoptOpenJDK)(build 25.292-b10, mixed mode)

 ~ javac -version
javac 1.8.0_292