PANR - HPC issues

[ewagajda]

> source R-3.2.2
> R

1.

> library(PANR)

> pan<-new("PAN", bm1=bm1)
> pan<-infer(pan, para=list(type="SNR", log=TRUE, sign=TRUE,  
cutoff=log(5)), filter=FALSE, verbose=TRUE)
> data(Bakal2007Cluster)
> pan<-buildPAN(pan, engine="RedeR", para=list(nodeColor=nodeColor, hideNeg=TRUE))

--use default args: nodeSumCols, nodeSumMethod -building RedeR graph ... -finished building RedeR graph ...

> library(RedeR)

***This is RedeR 1.18.1! For a quick start, please type 'vignette('RedeR')'. Supporting information is available at Genome Biology 13:R29, 2012, (doi:10.1186/gb-2012-13-4-r29).

> viewPAN(pan, what="graph") ................................................................................

The Java interface is not responding to initialization! Please, check whether Java is already installed in your machine (JRE version>=6). For a general diagnosis, re-run the 'calld' function with 'checkcalls=TRUE', for example: > calld(rdp, checkcalls=TRUE) Please report any eventual error message to us

2.

> inds<-sigModules(pan,pValCutoff=0.01, minSize=3, maxSize=100, sortby="pval", 
decreasing=FALSE)
> viewPAN(pan,what="pvclustModule", moduleID=inds)

................................................................................

The Java interface is not responding to initialization! Please, check whether Java is already installed in your machine (JRE version>=6). For a general diagnosis, re-run the 'calld' function with 'checkcalls=TRUE', for example: > calld(rdp, checkcalls=TRUE) Please report any eventual error message to us There were 50 or more warnings (use warnings() to see the first 50)

> warnings()

Warning messages: 1: In .Call("R_igraph_subgraph", graph, as.igraph.vs(graph, ... : At structural_properties.c:1945 :igraph_subgraph is deprecated from igraph 0.6, use igraph_induced_subgraph instead

3. > viewNestedModules(pan,pValCutoff=0.05,minSize=3,maxSize=100) ................................................................................

The Java interface is not responding to initialization! Please, check whether Java is already installed in your machine (JRE version>=6). For a general diagnosis, re-run the 'calld' function with 'checkcalls=TRUE', for example:> calld(rdp, checkcalls=TRUE) Please report any eventual error message to us

[wjurkowski]

I got an error whilst installing PANR. Did you load libcurl prior to installing PANR and launching it later? source libcurl-7.32.0

[wjurkowski]

On the other hand the interactive visualisation wont work over the net. Are other functions of PANR working?

[wjurkowski]

if the problem persist let's test it locally

[ewagajda]

I didn't load libcurl prior to installing PANR. This is my log from PANR instalation

ssh software
source R-3.2.2
R 
source("http://bioconductor.org/biocLite.R")
biocLite("PANR")

BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.2 (2015-08-14). Installing package(s) ‘PANR’ trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/PANR_1.16.0.tar.gz' Content type 'application/x-gzip' length 2074406 bytes (2.0 MB)

downloaded 2.0 MB

• installing source package ‘PANR’ ... * R * data * inst * preparing package for lazy loading \ help ** installing help indices * building package indices * installing vignettes * testing if installed package can be loaded
• DONE (PANR)

The downloaded source packages are in ‘/tmp/RtmpGY64VW/downloaded_packages’ Old packages: 'robustbase', 'ape', 'BH', 'Cairo', 'corrplot', 'DBI', 'devtools', 'evaluate', 'fields', 'formatR', 'git2r', 'highr', 'Hmisc', 'jsonlite', 'knitr', 'Matrix', 'nlme', 'openssl', 'phyloseq', 'plotrix', 'Rcpp', 'RcppArmadillo', 'RCurl', 'scatterplot3d', 'stringi', 'survival', 'testthat' Update all/some/none? [a/s/n]: n

[ewagajda]

Yes, other functions are working, it's just the graphics that don't.