Hello, I am getting an error while trying to execute the example code for the oposSOM package as reported by

?opossom.run

My code is the following:

# Example with artificial data
env <- opossom.new(list(dataset.name="Example",
                        error.model="all.samples",
                        dim.1stLvlSom=20,
                        dim.2ndLvlSom=20,
                        geneset.analysis=TRUE))

env$indata <- matrix(runif(1000), 100, 10)

opossom.run(env)

And this is the output:

[2015-11-23 13:41:45][INFO] Started: Mon 23 Nov 2015 01:41:45 PM
[2015-11-23 13:41:45][INFO] Setting: Example
[2015-11-23 13:41:45][INFO] 1SOM Dim: 20
[2015-11-23 13:41:45][INFO] 2SOM Dim: 20
[2015-11-23 13:41:45][WARN] No rownames found. Set them to 1,2,3,4...
[2015-11-23 13:41:45][WARN] No colnames found. Set them to 1,2,3,4...
[2015-11-23 13:41:46][INFO] Load Annotation Data
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
[2015-11-23 13:41:46][WARN] biomaRt seems to be down.
[2015-11-23 13:41:46][WARN] Disabling geneset analysis.
[2015-11-23 13:41:46][INFO] Processing SOM. This may take several time until next notification.
[2015-11-23 13:41:47][INFO] Remaining ~ 1 min ~ 0 h
[2015-11-23 13:41:48][INFO] Saving environment image: Example pre.RData
[2015-11-23 13:41:48][INFO] Processing Differential Expression
[2015-11-23 13:41:48][INFO] Processing Single Genes
[2015-11-23 13:41:48][INFO] [                                                ][2015-11-23 13:41:48][INFO] [#############################                   ][2015-11-23 13:41:48][INFO] [###############################                 ][2015-11-23 13:41:48][INFO] [#################################               ][2015-11-23 13:41:48][INFO] [###################################             ][2015-11-23 13:41:48][INFO] [####################################            ][2015-11-23 13:41:48][INFO] [######################################          ][2015-11-23 13:41:48][INFO] [########################################        ][2015-11-23 13:41:48][INFO] [##########################################      ][2015-11-23 13:41:48][INFO] [############################################    ][2015-11-23 13:41:48][INFO] [##############################################  ][2015-11-23 13:41:48][INFO] [################################################][2015-11-23 13:41:48][INFO] [################################################]
[2015-11-23 13:41:48][INFO] Writing: Example - Results/LPE/all_samples.bmp
[2015-11-23 13:41:48][INFO] Processing Metagenes
[2015-11-23 13:41:48][INFO] [                                                ][2015-11-23 13:41:48][INFO] [###################                             ][2015-11-23 13:41:48][INFO] [######################                          ][2015-11-23 13:41:48][INFO] [#########################                       ][2015-11-23 13:41:48][INFO] [############################                    ][2015-11-23 13:41:48][INFO] [###############################                 ][2015-11-23 13:41:48][INFO] [##################################              ][2015-11-23 13:41:48][INFO] [####################################            ][2015-11-23 13:41:48][INFO] [#######################################         ][2015-11-23 13:41:48][INFO] [##########################################      ][2015-11-23 13:41:48][INFO] [#############################################   ][2015-11-23 13:41:48][INFO] [################################################][2015-11-23 13:41:48][INFO] [################################################]
[2015-11-23 13:41:48][INFO] Writing: Example - Results/LPE/Sigma_LPE.pdf
[2015-11-23 13:41:48][INFO] Detecting Spots
[2015-11-23 13:41:49][INFO] Plotting Sample Portraits
[2015-11-23 13:41:49][INFO] Writing: Example - Results/Expression Portraits.pdf
[2015-11-23 13:41:49][INFO] Writing: Example - Results/Expression Portraits - alternative scales.pdf
[2015-11-23 13:41:49][INFO] Writing: Example - Results/Rank Maps.pdf
[2015-11-23 13:41:49][INFO] Processing Supporting Information
[2015-11-23 13:41:49][INFO] Writing: Example - Results/Supporting Maps&Profiles/Supporting Maps.pdf
[2015-11-23 13:41:50][INFO] Writing: Example - Results/Supporting Maps&Profiles/Entropy Profiles.pdf
[2015-11-23 13:41:50][INFO] Writing: Example - Results/Supporting Maps&Profiles/Topology Profiles.pdf
[2015-11-23 13:41:50][INFO] Processing 2nd level Metagene Analysis
[2015-11-23 13:41:50][INFO] Writing: Example - Results/2nd lvl Metagene Analysis/Similarity Analysis.pdf
[2015-11-23 13:41:53][INFO] Writing: Example - Results/2nd lvl Metagene Analysis/Correlation Analysis.pdf
Error in .Call("R_igraph_layout_kamada_kawai", graph, coords, maxiter,  : 
  At structural_properties.c:5235 : cannot run Bellman-Ford algorithm, Negative loop detected while calculating shortest paths

Apart from the initial BiomaRt error, which has been reported by others (things have changed recently with the Ensembl Biomart API), the last error prevents the function from producing the other results.

>sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                
[9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] oposSOM_1.4.0

loaded via a namespace (and not attached):
[1] lattice_0.20-33      ape_3.3              IRanges_2.2.9        XML_3.98-1.3         bitops_1.0-6         grid_3.2.0         
[7] GenomeInfoDb_1.4.3   nlme_3.1-122         DBI_0.3.1            stats4_3.2.0         magrittr_1.5         RSQLite_1.0.0      
[13] KernSmooth_2.23-15   som_0.3-5            pixmap_0.4-11        fdrtool_1.2.15       scatterplot3d_0.3-36 S4Vectors_0.6.6    
[19] fastICA_1.2-0        tools_3.2.0          Biobase_2.28.0       biomaRt_2.24.1       RCurl_1.95-4.7       igraph_1.0.1       
[25] parallel_3.2.0       BiocGenerics_0.14.0  AnnotationDbi_1.30.1