Question: Rcellminer failing to load because of rcdk
0
gravatar for zayed.albertyn
2.3 years ago by
zayed.albertyn0 wrote:

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   

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by zayed.albertyn0
Answer: Rcellminer failing to load because of rcdk
1
gravatar for cannin
2.3 years ago by
cannin20
United States
cannin20 wrote:

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. 

ADD COMMENTlink written 2.3 years ago by cannin20
Answer: Rcellminer failing to load because of rcdk
0
gravatar for zayed.albertyn
2.3 years ago by
zayed.albertyn0 wrote:

>Specifically, the instructions by Nasser Sep 5 '16

That worked great. I have it running now.

ADD COMMENTlink written 2.3 years ago by zayed.albertyn0
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