Hi All

I am trying to use Rcellminer on mac os X. My installation runs all the way through but when I try to load the package

library(rcellminer)

It crashes with the following error:

library(rcellminer)
Loading required package: rcdk
JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Error : .onLoad failed in loadNamespace() for 'rcdklibs', details:
  call: .jinit(classpath = c(jars))
  error: JNI_GetCreatedJavaVMs returned -1

Error: package ‘rcdk’ could not be loaded

I even tried setting my $JAVA_HOME using Sys.Setenv() but to no avail. 

My current system java is :

openjdk version "1.8.0_92"

OpenJDK Runtime Environment (Zulu 8.15.0.1-macosx) (build 1.8.0_92-b15)

OpenJDK 64-Bit Server VM (Zulu 8.15.0.1-macosx) (build 25.92-b15, mixed mode)

Has anybody experienced a similar issue?

Thanks.

Z

P.S. below is my environment details

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rJava_0.9-8          rcellminerData_1.4.2 fingerprint_3.5.4    Biobase_2.32.0      
 [5] BiocGenerics_0.18.0  devtools_1.12.0      rCharts_0.4.5        ggplot2_2.2.1       
 [9] data.table_1.10.4    shiny_1.0.0         

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9      plyr_1.8.4       iterators_1.0.8  tools_3.3.0      digest_0.6.12   
 [6] memoise_1.0.0    tibble_1.2       gtable_0.2.0     lattice_0.20-34  png_0.1-7       
[11] yaml_2.1.14      withr_1.0.2      grid_3.3.0       R6_2.2.0         RJSONIO_1.3-0   
[16] whisker_0.3-2    scales_0.4.1     htmltools_0.3.5  itertools_0.1-3  assertthat_0.1  
[21] mime_0.5         xtable_1.8-2     colorspace_1.3-2 httpuv_1.3.3     lazyeval_0.2.0  
[26] munsell_0.4.3   

The best set of instructions I've seen for installing Java on OSX in a way that is compatible with Java-based libraries like rJava, rcdk, etc on OSX Yosemite and above are here: 

https://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite

Specifically, the instructions by Nasser Sep 5 '16, just do not worry about the RWeka parts unless that's an important package for you. Make sure rcdk can load otherwise there is no chance rcellminer will. 

>Specifically, the instructions by Nasser Sep 5 '16

That worked great. I have it running now.