new readme updates

README.org

@@ -81,8 +81,17 @@
 
 ** Major Dependency Hell
    Among Shinyscreen dependencies, ~mzR~ and ~rcdk~ have been known 
-   to cause major installation issues. Detailed explanation on how 
-   to tackle these is available [[https://github.com/schymane/RChemMass/blob/master/README_installation.txt][here]].
+   to cause major installation issues.
+   To install the dependencies use the following script
+   #+BEGIN_SRC R
+     BiocManager::install(c(curl","rsvg","enviPat","rJava", "fingerprint", "png", "rcdk","mzR","rcdklibs"), dependencies=TRUE))
+   #+END_SRC
+  
+   -However the major issue in installing the dependencies is loading ~rjava~ library (essential rcdk functionality)
+   -Install the latest Java versions: [[https://www.java.com/en/][Download]]
+   -Ensure 32 bit and 64 bit versions are available for 64 bit systems.Check in C:\Program Files\Java and C:\Program Files (x86)\Java.
+   -Test if the library is loaded properly and proceed with the installation of ~RMassBank~ and ~RChemMass~.
+   -Detailed explanation on how to tackle these is available [[https://github.com/schymane/RChemMass/blob/master/README_installation.txt][here]].
 
 * Running Shinyscreen
   Provided Shinyscreen is successfully installed this snippet will

[Todor Kondic]

This looks good to me. What do you think @emma.schymanski ?

[Emma Schymanski]

Yes, looks good! Thanks @anjana.elapavalore

Are there any updates I should do to RChemMass? [like BiocManager - any others?]

[Anjana Elapavalore]

except for BiocManager, I don't find any additional changes in that

[Emma Schymanski]

Do we need to add this too?

install.packages("installr")
library("installr")
install.Rtools()

[Anjana Elapavalore]

This code made rtools installation pretty simpler for me. Just in case if needed you can refer to this

[Emma Schymanski]

Done ;-)

https://github.com/schymane/RChemMass/commit/91fe3a7f4c4cb0b187eaa7c53e0f3ca5beafb30b