Synchronizing R system settings from Terminal, GUI and RStudio - r

Question

My problem on my MacOS is that I can use R from GUI (aka console, downloaded from CRAN), Terminal or from RStudio but I cannot have them function in the same way.
Specific example is I can use rJava on Terminal and RStudio but not on GUI. Similar stuff happens for Rmarkdown pdf outputs. I usually get errors from GUI but everything is fine on Terminal or RStudio. How do I update R GUI settings to the same as Terminal's?
ps. For instance R CMD javareconf command handled the Terminal R but not R GUI.
edit: It is not actually something that requires a minimal working example but let's try library(rJava) after installing it.
R Called from Terminal (same with RStudio)
No problems.
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0
R GUI
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0
Some differences between Sys.getenv() are GUI has the following extra
LD_LIBRARY_PATH :#JAVA_LD#
DYLD_LIBRARY_PATH /Library/Java/JavaVirtualMachines/jdk-10.0.1.jdk/Contents/Home/lib/server
Brief update: I was able to correct Rmarkdown situation by using this link and reading help by writing ?Startup on R console. Changed the Renviron file on my R.home()/etc/. But still no rJava.

Answer 1

For R Markdown problem, I managed to handle it by adding a ~/.Renviron file and defining PATH parameter with the value I got from Terminal's Sys.getenv() parameters.
The only thing that worked for rJava for High Sierra is the following answer (changed the version to 3.5 though)
https://stackoverflow.com/a/47685001/3608936