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ropensci / tabulapdf

Bindings for Tabula PDF Table Extractor Library
https://docs.ropensci.org/tabulapdf/
Apache License 2.0
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Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, : java.lang.IllegalAccessException: class RJavaTools cannot access a member of class java.util.ArrayList$Itr (in module java.base) with modifiers "public" #147

Closed NiccoloSalvini closed 4 months ago

NiccoloSalvini commented 2 years ago

Hi, I have a problem reading a pdf table. The link and the pdf document are not corrupted (e.g. pdftools::pdf_text() works fine, but I when I am trying to extract tables:

## rJava loads successfully
# install.packages("rJava")
library(rJava)
library(tabulizer)
out = extract_tables("https://www.aifa.gov.it/documents/20142/1626083/report_n.12_monitoraggio_antivirali_10.06.2022.pdf")

I get the following error:

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  : 
  java.lang.IllegalAccessException: class RJavaTools cannot access a member of class java.util.ArrayList$Itr (in module java.base) with modifiers "public"

with the following traceback:

6: stop(structure(list(message = "java.lang.IllegalAccessException: class RJavaTools cannot access a member of class java.util.ArrayList$Itr (in module java.base) with modifiers \"public\"", 
       call = .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", 
           cl, .jcast(if (inherits(o, "jobjRef") || inherits(o, 
               "jarrayRef")) o else cl, "java/lang/Object"), .jnew("java/lang/String", 
               method), j_p, j_pc, use.true.class = TRUE, evalString = simplify, 
           evalArray = FALSE), jobj = new("jobjRef", jobj = <pointer: 0x1506acf38>, 
           jclass = "java/lang/IllegalAccessException")), class = c("IllegalAccessException", 
   "ReflectiveOperationException", "Exception", "Throwable", "Object", 
   "error", "condition")))
5: .jcheck(silent = FALSE)
4: .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, 
       .jcast(if (inherits(o, "jobjRef") || inherits(o, "jarrayRef")) o else cl, 
           "java/lang/Object"), .jnew("java/lang/String", method), 
       j_p, j_pc, use.true.class = TRUE, evalString = simplify, 
       evalArray = FALSE)
3: .jrcall(x, name, ...)
2: guessesIterator$hasNext()
1: extract_tables("https://www.aifa.gov.it/documents/20142/1626083/report_n.12_monitoraggio_antivirali_10.06.2022.pdf", 
       encoding = "UTF-8")

devtools::session_info()

─ Session info ─
 setting  value
 version  R version 4.2.0 (2022-04-22)
 os       macOS Monterey 12.4
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Rome
 date     2022-06-23
 rstudio  2022.02.2+485 Prairie Trillium (desktop)
 pandoc   NA

─ Packages ─
 package       * version date (UTC) lib source
 assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.2.0)
 brio            1.1.3   2021-11-30 [1] CRAN (R 4.2.0)
 cachem          1.0.6   2021-08-19 [1] CRAN (R 4.2.0)
 callr           3.7.0   2021-04-20 [1] CRAN (R 4.2.0)
 cli             3.3.0   2022-04-25 [1] CRAN (R 4.2.0)
 crayon          1.5.1   2022-03-26 [1] CRAN (R 4.2.0)
 DBI             1.1.2   2021-12-20 [1] CRAN (R 4.2.0)
 desc            1.4.1   2022-03-06 [1] CRAN (R 4.2.0)
 devtools      * 2.4.3   2021-11-30 [1] CRAN (R 4.2.0)
 dplyr           1.0.9   2022-04-28 [1] CRAN (R 4.2.0)
 ellipsis        0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
 fansi           1.0.3   2022-03-24 [1] CRAN (R 4.2.0)
 fastmap         1.1.0   2021-01-25 [1] CRAN (R 4.2.0)
 fs            * 1.5.2   2021-12-08 [1] CRAN (R 4.2.0)
 generics        0.1.2   2022-01-31 [1] CRAN (R 4.2.0)
 glue            1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
 here          * 1.0.1   2020-12-13 [1] CRAN (R 4.2.0)
 lifecycle       1.0.1   2021-09-24 [1] CRAN (R 4.2.0)
 magrittr        2.0.3   2022-03-30 [1] CRAN (R 4.2.0)
 memoise         2.0.1   2021-11-26 [1] CRAN (R 4.2.0)
 pillar          1.7.0   2022-02-01 [1] CRAN (R 4.2.0)
 pkgbuild        1.3.1   2021-12-20 [1] CRAN (R 4.2.0)
 pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
 pkgload         1.2.4   2021-11-30 [1] CRAN (R 4.2.0)
 png             0.1-7   2013-12-03 [1] CRAN (R 4.2.0)
 prettyunits     1.1.1   2020-01-24 [1] CRAN (R 4.2.0)
 processx        3.6.0   2022-06-10 [1] CRAN (R 4.2.0)
 ps              1.7.0   2022-04-23 [1] CRAN (R 4.2.0)
 purrr           0.3.4   2020-04-17 [1] CRAN (R 4.2.0)
 R6              2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
 ragg          * 1.2.2   2022-02-21 [1] CRAN (R 4.2.0)
 remotes         2.4.2   2021-11-30 [1] CRAN (R 4.2.0)
 rJava         * 1.0-6   2021-12-10 [1] CRAN (R 4.2.0)
 rlang           1.0.2   2022-03-04 [1] CRAN (R 4.2.0)
 rprojroot       2.0.3   2022-04-02 [1] CRAN (R 4.2.0)
 sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
 systemfonts     1.0.4   2022-02-11 [1] CRAN (R 4.2.0)
 tabulizer     * 0.2.2   2022-06-22 [1] Github (ropensci/tabulizer@3049a79)
 tabulizerjars * 1.0.1   2022-06-22 [1] Github (ropensci/tabulizerjars@d1924e0)
 testthat        3.1.4   2022-04-26 [1] CRAN (R 4.2.0)
 textshaping     0.3.6   2021-10-13 [1] CRAN (R 4.2.0)
 tibble          3.1.7   2022-05-03 [1] CRAN (R 4.2.0)
 tidyselect      1.1.2   2022-02-21 [1] CRAN (R 4.2.0)
 usethis       * 2.1.6   2022-05-25 [1] CRAN (R 4.2.0)
 utf8            1.2.2   2021-07-24 [1] CRAN (R 4.2.0)
 vctrs           0.4.1   2022-04-13 [1] CRAN (R 4.2.0)
 withr           2.5.0   2022-03-03 [1] CRAN (R 4.2.0)

 [1] /Users/niccolo/Library/R/arm64/4.2/library
 [2] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library

───
jbryer commented 2 years ago

I am getting the same error. I have a job I run once a year. It worked fine last year. Following.

ggSamoora commented 2 years ago

I found a solution to this problem. You have to use an older version of JDK for this to work. I created a 10-minute tutorial on how to properly set up the Tabulizer package. You can find the YouTube video here

BastienNguyen commented 2 years ago

Can you please provide a osx method too?

ssingh13-rms commented 2 years ago

I found a solution to this problem. You have to use an older version of JDK for this to work. I created a 10-minute tutorial on how to properly set up the Tabulizer package. You can find the YouTube video here

What's the version of JDK you used?

drpedapati commented 2 years ago

Can you please provide a osx method too?

Go here and download Java 8 https://www.azul.com/downloads/?version=java-8-lts&package=jdk Recommend DMG package and install Uninstall any other Java VMs https://docs.azul.com/core/zulu-openjdk/uninstall/macos Check at terminal: javac -version javac 1.8.0_345

Now you should be able to run extract_tables

I'm not a java developer but the versioning is confusing

beatrizmilz commented 1 year ago

Thank you so much @drpedapati !! I use Mac OS, with M1 chip, and was having a hard time to install tabulizer. Your last tip, to uninstall other java VMs, and install Java 8, worked well!

Can you please provide a osx method too?

Go here and download Java 8 https://www.azul.com/downloads/?version=java-8-lts&package=jdk Recommend DMG package and install Uninstall any other Java VMs https://docs.azul.com/core/zulu-openjdk/uninstall/macos Check at terminal: javac -version javac 1.8.0_345

Now you should be able to run extract_tables

I'm not a java developer but the versioning is confusing

pachadotdev commented 1 year ago

Thanks! I had the exact same problem on Windows. I'll try to increase Tabula version in the source.

tomwagstaff-opml commented 11 months ago

Has anyone found a solution that doesn't involve rolling back the Java version? I haven't got admin permissions to do that...

pachadotdev commented 11 months ago

Has anyone found a solution that doesn't involve rolling back the Java version? I haven't got admin permissions to do that...

not yet

pachadotdev commented 5 months ago

works with OpenJDK11 now :)

pachadotdev commented 4 months ago

fixed in 1.0.5-3 (https://cran.r-project.org/package=tabulapdf)