tabulapdf extract_tables() error: java.lang.NoSuchMethodError

extract_tables() error: java.lang.NoSuchMethodError

Open jzadra opened this issue 7 years ago • 28 comments

I've just installed tabulizer from github. I'm using MacOS Sierra. I also installed the legacy java from the link given on the install instructions: https://support.apple.com/kb/DL1572?locale=en_US.

When I use extract_tables(), I get the following error:

f <- system.file("examples", "data.pdf", package = "tabulizer")
extract_tables(f)
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I

Mar 14 '17 17:03 jzadra

traceback()
7: stop(list(message = "java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I", 
       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 = <S4 object of class "jobjRef">))
6: .Call(RJavaCheckExceptions, silent)
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: spreadsheetExtractor$isTabular(page)
1: extract_tables(f)

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

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_0.1.24 ghit_0.2.17      stringr_1.1.0    lubridate_1.6.0  forcats_0.2.0    scales_0.4.1    
 [7] readxl_0.1.1     dplyr_0.5.0      purrr_0.2.2      readr_1.0.0      tidyr_0.6.1      tibble_1.2      
[13] ggplot2_2.2.1    tidyverse_1.1.1  knitr_1.15.1    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9         git2r_0.18.0        plyr_1.8.4          tools_3.3.2         jsonlite_1.3       
 [6] evaluate_0.10       nlme_3.1-128        gtable_0.2.0        lattice_0.20-34     png_0.1-7          
[11] psych_1.6.12        DBI_0.5-1           parallel_3.3.2      haven_1.0.0         rJava_0.9-8        
[16] httr_1.2.1          xml2_1.1.1          hms_0.3             grid_3.3.2          R6_2.2.0           
[21] foreign_0.8-67      reshape2_1.4.2      modelr_0.1.0        magrittr_1.5        tabulizerjars_0.9.2
[26] assertthat_0.1      mnormt_1.5-5        rvest_0.3.2         colorspace_1.3-2    stringi_1.1.2      
[31] lazyeval_0.2.0      munsell_0.4.3       broom_0.4.2

Mar 14 '17 17:03 jzadra

I'm facing the same issue on the same setup as @jzadra. Any thoughts on how to address this is greatly appreciated!

Mar 16 '17 17:03 soedr

Having the same issue here!

Mar 16 '17 20:03 jrcunning

@soedr @jrcunning Are you also on Mac? Versions?

Mar 17 '17 09:03 leeper

Yes, on Mac. I also installed the legacy java using the same link as @jzadra. Here is my Session Info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.3 (Sierra)

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_0.1.24

loaded via a namespace (and not attached):
[1] tabulizerjars_0.9.2 tools_3.3.1         rJava_0.9-8         png_0.1-7

Mar 17 '17 13:03 jrcunning

@jrcunning Thanks. Can you tell me what version of Java you installed? (The underlying java library - tabula - has some updates and it looks like they're causing Mac-specific issues.)

Mar 17 '17 17:03 leeper

@leeper Yes, on Mac. Followed same procedure as @jzadra and @jrcunning. Session info:

 R version 3.3.2 (2016-10-31)
 Platform: x86_64-apple-darwin13.4.0 (64-bit)
 Running under: macOS Sierra 10.12.3

 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_0.1.24   devtools_1.12.0

 loaded via a namespace (and not attached):
 [1] reshape2_1.4.2       rJava_0.9-8          haven_1.0.0          lattice_0.20-34      colorspace_1.3-2     ghit_0.2.17          foreign_0.8-67       withr_1.0.2          DBI_0.5-1           
 [10] modelr_0.1.0         readxl_0.1.1         plyr_1.8.4           stringr_1.1.0        munsell_0.4.3        gtable_0.2.0         rvest_0.3.2          leaps_3.0            psych_1.6.12        
 [19] memoise_1.0.0        labeling_0.3         knitr_1.15.1         forcats_0.2.0        parallel_3.3.2       curl_2.3             broom_0.4.2          Rcpp_0.12.9          tabulizerjars_0.9.2 
 [28] scales_0.4.1         flashClust_1.01-2    scatterplot3d_0.3-38 jsonlite_1.2         mnormt_1.5-5         png_0.1-7            hms_0.3              digest_0.6.12        stringi_1.1.2       
 [37] grid_3.3.2           tools_3.3.2          magrittr_1.5         lazyeval_0.2.0       cluster_2.0.5        crayon_1.3.2         MASS_7.3-45          xml2_1.1.0           lubridate_1.6.0     
 [46] assertthat_0.1       httr_1.2.1           R6_2.2.0             nlme_3.1-128         git2r_0.18.0

Mar 17 '17 21:03 soedr

Java SE 6

Mar 17 '17 21:03 jrcunning

Facing the same issue. Would appreciate help.

Mar 30 '17 20:03 ahassanali

It seems the latest version of the tabula library is likely the issue. Consider re-installing an older version of tabulizerjars with, for example:

ghit::install_github("ropensci/[email protected]", verbose = TRUE)

Mar 31 '17 11:03 leeper

I installed tabulizerjarms v0.9.0 but still getting the same error:

> traceback()
7: stop(list(message = "java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I", 
       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 = <S4 object of class "jobjRef">))
6: .Call(RJavaCheckExceptions, silent)
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: spreadsheetExtractor$isTabular(page)
1: extract_tables("data/raw/Appendix D. Counts of Scleractinians, Octocorals and Sponges during Base....pdf", 
       columns = columns, pages = p, guess = F) at #9


> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.3 (Sierra)

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_0.1.24    tabulizerjars_0.9.0 stringr_1.1.0       reshape2_1.4.1     

loaded via a namespace (and not attached):
[1] magrittr_1.5  plyr_1.8.4    tools_3.3.1   Rcpp_0.12.10  stringi_1.1.1 git2r_0.15.0  ghit_0.2.12  
[8] rJava_0.9-8   png_0.1-7

Apr 04 '17 13:04 jrcunning

Hey @leeper, tabula author here. Would love to help sorting this issue out, as the latest versions have significant perfomance and accuracy improvements.

Would it be possible to get a code snippet that reproduces the issue?

Thanks.

Apr 07 '17 16:04 jazzido

I have the same problem.

Version

R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

Code from ?extract_files

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

Traceback

6.
stop(structure(list(message = "java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I", 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", ...
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, ...
3.
.jrcall(x, name, ...)
2.
spreadsheetExtractor$isTabular(page)
1.
extract_tables(f)

Thank you

Apr 09 '17 16:04 wtro

Version

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.3 (Sierra)

Code

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

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I

traceback()

7: stop(list(message = "java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I", 
       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 = <S4 object of class "jobjRef">))
6: .Call(RJavaCheckExceptions, silent)
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: spreadsheetExtractor$isTabular(page)
1: extract_tables(f)

Apr 11 '17 13:04 jkeuskamp

@leeper I'm quite sure that this only happens in Java 6.

Apr 11 '17 15:04 jazzido

Tabula-0.9.2.jar renders the same error as generated by tabulizer when Java 6 is the default JRE (see below). This is solved when switching to Java 8; unfortunately this does not make tabulizer work.

Exception in thread "main" java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I
	at technology.tabula.TextChunk.isLtrDominant(TextChunk.java:179)
	at technology.tabula.TextElement.mergeWords(TextElement.java:271)
	at technology.tabula.TextElement.mergeWords(TextElement.java:105)
	at technology.tabula.extractors.BasicExtractionAlgorithm.extract(BasicExtractionAlgorithm.java:46)
	at technology.tabula.CommandLineApp$TableExtractor.extractTablesBasic(CommandLineApp.java:385)
	at technology.tabula.CommandLineApp$TableExtractor.extractTables(CommandLineApp.java:359)
	at technology.tabula.CommandLineApp.extractFile(CommandLineApp.java:166)
	at technology.tabula.CommandLineApp.extractFileTables(CommandLineApp.java:123)
	at technology.tabula.CommandLineApp.extractTables(CommandLineApp.java:104)
	at technology.tabula.CommandLineApp.main(CommandLineApp.java:74)

Apr 13 '17 15:04 jkeuskamp

@jkeuskamp Can you run java -version on a terminal? I'd like to confirm if that error occurs only with Java 6.

Apr 13 '17 15:04 jazzido

It is indeed Java 6: java version "1.6.0_65" Java(TM) SE Runtime Environment (build 1.6.0_65-b14-468-11M4833) Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-468, mixed mode)

Apr 13 '17 16:04 jkeuskamp

Thanks @jkeuskamp. Can't help you much about tabulizer, but tabula itself will work under a newer version of the Java virtual machine (7 or 8). Bear in mind that Java 6 has stopped receiving updates and support since 2013.

I'd recommend that you update your Java installation and try again.

Apr 13 '17 16:04 jazzido

@leeper @jzadra @jazzido
This solved the issue for me: I Installed JVM 8 and pointed RStudio to its installation as described here

to make tabulizer use JVM 8, edit the file ~/.profile and set the following env variables:

export JAVA_HOME=`/usr/libexec/java_home -v 1.8
export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/server

then restart macOS or set the variables manually and restart RStudio.

Apr 14 '17 09:04 jkeuskamp

After trying the fix that solved things for jkeuskamp, I unfortunately still receive the "java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I" error.

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.4

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_0.1.24 rJava_0.9-8      tidyr_0.6.1      magrittr_1.5     dplyr_0.5.0     

loaded via a namespace (and not attached):
 [1] tabulizerjars_0.9.2 R6_2.2.0            assertthat_0.2.0    DBI_0.6-1          
 [5] tools_3.3.3         tibble_1.3.0        Rcpp_0.12.10        git2r_0.18.0       
 [9] ghit_0.2.17         png_0.1-7          

> traceback()
7: stop(list(message = "java.lang.NoSuchMethodError: java.lang.Integer.compare(II)I", 
       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 = <S4 object of class "jobjRef">))
6: .Call(RJavaCheckExceptions, silent)
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: spreadsheetExtractor$isTabular(page)
1: extract_tables(f2, pages = 2)

Apr 14 '17 22:04 supermdat

@supermdat could you confirm that java 8 is indeed called from R? You can check this by typing

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

this should return someting like

"1.8.0_121-b13"

The second number tells you whether java 6/7/8 is called.

Apr 15 '17 08:04 jkeuskamp

Thanks very much, @jkeuskamp . That is indeed the difference.

Running java -version from terminal gives:

java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

However, running this from within RStudio gives:

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
"1.6.0_65-b14-468-11M4833"

I've done some searching but don't understand well how to have R call Java 8. I'll continue researching, but would appreciate any tips.

Apr 15 '17 15:04 supermdat

@leeper Just noticed that the README.Rmd mentions:

On Mac OS, you may need to install a particular version of Java prior to attempting to install tabulizer.

You probably want to remove this line, as tabulizer now requires Java 7/8

Apr 16 '17 14:04 jkeuskamp

@supermdat

Found similar issue on rJava GitHub

Managed to force rJava to use 1.8 by running R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers then reinstalling rJava from source with install.packages("rJava", "http://rforge.net/", type="source")

If you run into issues then loading rJava with something similar to error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so':

you then need to link the files together using: source sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib

And finally, it should load and show 1.8, which on my system meant I could run tabulizer successfully(!),

Apr 20 '17 09:04 lissahyacinth

Hi all,

Would there be any way at all of getting tabulizer to work with Java 6? I'm having the above NoSuchMethodError issue but on Windows with Java 6 installed (unfortunately can't update Java very easily as it's a work computer without admin rights) Perhaps an older version of tabulizer and/or tabulizerjars?

Thanks for any help anyone can offer!

Apr 20 '17 16:04 peterblair

@peterblair You can definitely try pulling an older version of tabulizerjars; the versions are all available as releases on GitHub and they are numbered to align with tabula-java release numbers, e.g.: ghit::install_github("ropensci/[email protected]")

Apr 20 '17 20:04 leeper

Just for info, installing tabulizerjars v0.8.0 works with Java 6 on Windows. Thanks very much!

Apr 21 '17 09:04 peterblair

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