First example: Permission denied

[azzaea]

Hello,

Thank you for providing this package. I just installed the package, but keep getting a Permission denied error as below upon running the first example in the README. Would you kindly advise?

Thank you, Azza

> plot( 
+   x = x
+   # vector = TRUE
+ )
sh: 1: : Permission denied
[1] 127
Warning message:
In system2(command = java_bin, args = paste(java_opt, cmd, plantuml_opt),  :
  error in running command

Here are my session info:

> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] flow_0.0.2   plantuml_0.4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        compiler_4.0.5    pillar_1.6.0      R.utils_2.10.1    R.methodsS3_1.8.1
 [6] prettyunits_1.1.1 remotes_2.3.0     tools_4.0.5       digest_0.6.27     testthat_3.0.2   
[11] pkgbuild_1.2.0    pkgload_1.2.1     jsonlite_1.7.2    R.cache_0.15.0    memoise_2.0.0    
[16] lifecycle_1.0.0   tibble_3.1.1      pkgconfig_2.0.3   png_0.1-7         rlang_0.4.11     
[21] rstudioapi_0.13   cli_2.5.0         yaml_2.2.1        nomnoml_0.2.3     curl_4.3         
[26] fastmap_1.1.0     withr_2.4.2       styler_1.4.1      htmlwidgets_1.5.3 desc_1.3.0       
[31] fs_1.5.0          vctrs_0.3.8       devtools_2.4.1    rprojroot_2.0.2   grid_4.0.5       
[36] grImport_0.9-3    glue_1.4.2        R6_2.5.0          processx_3.5.2    fansi_0.4.2      
[41] XML_3.99-0.6      pacman_0.5.1      sessioninfo_1.1.1 callr_3.7.0       purrr_0.3.4      
[46] magrittr_2.0.1    htmltools_0.5.1.1 backports_1.2.1   ps_1.6.0          ellipsis_0.3.2   
[51] usethis_2.0.1     utf8_1.2.1        cachem_1.0.4      crayon_1.4.1      R.oo_1.24.0      
> 

[rkrug]

Permissions are usually local system specific. You should look if you can execute plantuml from the command line as described here.

If this runs, the function which executes the system2() call is plantuml_run (), so you could step through that function to get the command executed and that try that one from the terminal. This is in line https://github.com/rkrug/plantuml/blob/23db23cd9b99975eb9d2402a6e95c0efea7c0b9b/R/plantuml_run.R#L65

Let me know if this does not help, and I can take a closer look.

[azzaea]

Thank you much for the hint and help.

I looked around a bit, and the problem is now solved on my system (but I'm not clear on why- I haven't modified the package internally or particularly installed plantuml-related package). Nonetheless, here is what I did:

• Run plantuml_update() and download an updated jar.

> plantuml_update()
trying URL 'https://sourceforge.net/projects/plantuml/files/latest/download'
Content type 'application/java-archive' length 8346090 bytes (8.0 MB)
==================================================
downloaded 8.0 MB

[1] "/home/azza/.cache/R/plantuml/jar/plantuml.jar"

• Check the jar has the right permissions:

$ ll -h /home/azza/.cache/R/plantuml/jar/plantuml.jar
-rw-rw-r-- 1 azza azza 8.0M May 25 04:00 /home/azza/.cache/R/plantuml/jar/plantuml.jar
$ java -jar /home/azza/.cache/R/pl
antuml/jar/plantuml.jar -help
Usage: java -jar plantuml.jar [options] -gui
        (to execute the GUI)
    or java -jar plantuml.jar [options] [file/dir] [file/dir] [file/dir]
        (to process files or directories)
:
:

• Change the permissions on this jar (manually):

$ chmod +x  /home/azza/.cache/R/plantuml/jar/plantuml.jar

• Run the jar from R for the first example- it works, and a plot is generated

> plot( 
+     x = x
+     # vector = TRUE
+ )
[1] 0

• As a sanity check, remove the jar, run the plantuml_update() function again to re-download, check the permissions of the jar

  • The jar downloaded in the same location, with the same read-only permissions as before

• Run the first example without changing permissions

  • The example still works

Again, thank you much. Please feel free to close

[rkrug]

Good to hear that it is working now.