Catastrophic error with r-causal javax.xml.documentbuilder

[kingfish777]

Distributor ID: Ubuntu
Description: Ubuntu 16.04.2 LTS
Release: 16.04
Codename: xenial

# note: this works, well, doesn't work, that is, it breaks with "real" (read: "truthy") data as well =>
> library(rcausal)
> a <- c(1,1,1,0,0,0)
> b <- c(1,1,1,1,0,0)
> c <- c(0,0,0,1,0,0)
> dat <- data.frame(a,b,c)
> fges.discrete(dat)
Datasets:
dat 

Error in .jnew("edu/cmu/tetrad/search/Fges", score) : 
  java.lang.NoClassDefFoundError: Could not initialize class edu.cmu.tetrad.util.TetradLogger
> pcmax(dat)
Error in .jnew("edu/cmu/tetrad/search/IndTestFisherZ", tetradData, significance) : 
  javax.xml.parsers.FactoryConfigurationError: Provider for class javax.xml.parsers.DocumentBuilderFactory cannot be created

Seeing similar issue in Java API.
Java versions: 9ea, 8u121, 8u111, 7, both oracle and openjdk.
Not sure what has happened. 8/

[kingfish777]

System: Ubuntu 16.04, bioconductor 3.3
The following attempts at fixing issue were made to no avail:

• Tried update-alternatives route with oracle java 7/8 and openjdk 7/8, jdk 9ea.
• Tried removing all R packages (including bioconductor), doing apt autoremove and re-installing R afresh
• Tried setting up local r-causal-master, importing fresh tetrad-cmd-lib from 6.01 snapshot (the latest snapshot to which I have access)
• And the usual R fixes:
  -- recompiled all packages
  -- R CMD javareconf
  -- messed with environment variables (LD_PATH_LIBRARY), Sys.setenv(LD_...
  -- sudo ldconfig, etc.

HELP!!!

[kingfish777]

Resolved with fresh Ubuntu installation. Whew!

[kingfish777]

potential bioconductor 3.4 incompatibility (rJava)
With this version, rcausal failed:

> f <- fges.discrete(dat)
node_names:  a 
value: [1] 0 1

node_names:  b 
value: [1] 0 1

node_names:  c 
value: [1] 0 1

node_names:  d 
value: [1] 0 1

Datasets:
dat 
Error in .jnew("edu/cmu/tetrad/search/Fges", score) : 
  java.lang.NoClassDefFoundError: Could not initialize class edu.cmu.tetrad.util.TetradLogger

> biocVersion()
[1] ‘3.4’

However, it works fine with older bioc:

> biocVersion()
[1] ‘3.2’

[amurrayw]

I reproduced the bug in a fresh install of Linux Mint 18.1 Serena (based on Ubuntu Xenial), R version 3.4.0, biocVersion 3.5

Both of the first two examples posted in the README file (continuous and discrete runs of fges) fail with:

Error in .jnew("edu/cmu/tetrad/search/Fges", score) :
java.lang.NoClassDefFoundError: Could not initialize class edu.cmu.tetrad.util.TetradLogger

Traceback output (for fges.discrete) is:

4: stop(list(message = "java.lang.NoClassDefFoundError: Could not initialize class edu.cmu.tetrad.util.TetradLogger",
call = .jnew("edu/cmu/tetrad/search/Fges", score), jobj = <S4 object of class "jobjRef">))
3: .External(RcreateObject, class, ..., silent = silent)
2: .jnew("edu/cmu/tetrad/search/Fges", score)
1: fges.discrete(df = audiology, structurePrior = 1, samplePrior = 1,
maxDegree = -1, faithfulnessAssumed = TRUE, numOfThreads = 2,
verbose = TRUE)