I am trying to scrape tables from a PDF but from my local directory rather than from a web-browser (as it is not opening directly into a browser). Yet, I download the pdf onto my local directory and trying from there to read my tables only!
When I run my code:
PATH <-"C:\\Users\\gabrielburcea\\Rprojects\\Reports_scraping\\data_scraped\\icnarc_29052020\\icnarc_200529.pdf"
test <- extract_tables(PATH, output = "data.frame", pages = c(10, 11))
I get the following error which I cannot find anywhere on internet:
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", .jfindClass(class), :
java.io.FileNotFoundException: /Library/Frameworks/R.framework/Versions/3.6/Resources/library (Is a directory)
Is there a way to solve this issue?
The .pdf I am trying to scrape has been downloaded to my computer from the this website.
The report is titled ICNARC COVID-19 report 2020-05-29.pdf and can be downloaded using the link of the right-side of the page.
Below is the output of traceback() after I've received my error message.
8: stop(list(message = "java.io.FileNotFoundException: /Library/Frameworks/R.framework/Versions/3.6/Resources/library (Is a directory)",
call = .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance",
.jfindClass(class), .jarray(p, "java/lang/Object", dispatch = FALSE),
.jarray(pc, "java/lang/Class", dispatch = FALSE), evalString = FALSE,
evalArray = FALSE, use.true.class = TRUE), jobj = new("jobjRef",
jobj = <pointer: 0x7fd1ba0972b0>, jclass = "java/io/FileNotFoundException")))
7: .jcheck(silent = FALSE)
6: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", .jfindClass(class),
.jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc,
"java/lang/Class", dispatch = FALSE), evalString = FALSE,
evalArray = FALSE, use.true.class = TRUE)
5: .J(Class@name, ...)
4: new(J("java.io.FileInputStream"), name <- localfile)
3: new(J("java.io.FileInputStream"), name <- localfile)
2: load_doc(file, password = password, copy = copy)
1: extract_tables(PATH, output = "data.frame", pages = c(10, 11))
and sessionInfo() returns this:
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.5 purrr_0.3.3 readr_1.3.1 tidyr_1.0.3 tibble_3.0.1
[8] ggplot2_3.3.0 tidyverse_1.3.0 tabulizer_0.2.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 cellranger_1.1.0 pillar_1.4.3 compiler_3.6.1 dbplyr_1.4.2
[6] tools_3.6.1 lubridate_1.7.4 jsonlite_1.6 lifecycle_0.2.0 gtable_0.3.0
[11] nlme_3.1-140 lattice_0.20-38 pkgconfig_2.0.2 png_0.1-7 rlang_0.4.6
[16] reprex_0.3.0 cli_2.0.2 DBI_1.0.0 rstudioapi_0.11 haven_2.2.0
[21] rJava_0.9-12 withr_2.1.2 xml2_1.3.2 httr_1.4.1 fs_1.3.1
[26] hms_0.5.3 generics_0.0.2 vctrs_0.3.0 grid_3.6.1 tidyselect_1.1.0
[31] glue_1.3.1 R6_2.4.0 fansi_0.4.0 readxl_1.3.1 modelr_0.1.8
[36] magrittr_1.5 scales_1.0.0 tabulizerjars_1.0.1 backports_1.1.4 ellipsis_0.3.0
[41] rvest_0.3.5 assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.6 munsell_0.5.0
[46] broom_0.5.6 crayon_1.3.4
Thanks in advance for any help!
As discussed in comments, code is working fine on windows.
library(tabulizer)
link <- "https://www.icnarc.org/DataServices/Attachments/Download/8419d345-c7a1-ea11-9126-00505601089b"
dfr.list <- extract_tables(link, output="data.frame", pages=10:11)
To get every table out of the list use list2env where you set env=ironment to .GlobalEnv which is your workspace getwd(). Beforehand you need to give the unnamed list names.
names(dfr.list) <- paste0("dfr", 1:length(dfr.list)) ## give names
list2env(dfr.list, envir=.GlobalEnv) ## put to environment
ls()
# [1] "dfr.list" "dfr1" "dfr2" "dfr3" "link"
# [2] "tables.list"
.pdf extraction often is not perfect and we have to clean the data afterwards. To improve the result try to play around with the area=, columns=, and options of extract_tables, read the help page ?extract_tables, consult the documentation.