Question: DiffCorr: cannot run Bellman-Ford algorithm, Negative loop detected while calculating shortest paths
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gravatar for zhang.jianhai
4 months ago by
zhang.jianhai0 wrote:

Hello,

I am running the package DiffCorr, and following the tutorial: https://application.wiley-vch.de/books/sample/3527339582_c01.pdf.

In the page 15 of the tutorial, an error happened as following:

plot(g1, vertex.size=3, edge.width=3, vertex.color=ifelse + (igraph::degree(g1)>20,"Magenta","Green"),
+ vertex.label="", layout=layout.kamada.kawai)
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

When I skip the above error, the following 2 steps run well:

g2 <- delete.vertices(g2, which(igraph::degree(g2)<1))
plot(g2, vertex.size=3, edge.width=3, vertex.color=ifelse + (igraph::degree(g2)>20,"Magenta","Green"), + vertex.label="", layout=layout.kamada.kawai)

g2.fc <- fastgreedy.community(g2)

But this step gave error again:

g1.fc <- fastgreedy.community(g1)

Error in .Call("R_igraph_community_fastgreedy", graph, as.logical(merges), : At fast_community.c:547 : weights must be positive, Invalid value

And the session Information is:

sessionInfo()
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/R/3.4.0/lib64/R/lib/libRblas.so LAPACK: /bigdata/bioinfo/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/R/3.4.0/lib64/R/lib/libRlapack.so locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages: [1] spatstat_1.51-0 rpart_4.1-11 nlme_3.1-131
[4] BiocInstaller_1.26.0 genefilter_1.58.1 ath1121501cdf_2.18.0 [7] affy_1.54.0 GEOquery_2.42.0 DiffCorr_0.4.1
[10] multtest_2.32.0 fdrtool_1.2.15 igraph_1.0.1
[13] pcaMethods_1.68.0 Biobase_2.36.2 BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.11 compiler_3.4.0 bitops_1.0-6
[4] tools_3.4.0 zlibbioc_1.22.0 goftest_1.1-1
[7] digest_0.6.12 bit_1.1-12 annotate_1.54.0
[10] RSQLite_2.0 memoise_1.1.0 preprocessCore_1.38.1 [13] tibble_1.3.3 lattice_0.20-35 mgcv_1.8-17
[16] rlang_0.1.1 Matrix_1.2-10 DBI_0.7
[19] httr_1.2.1 spatstat.utils_1.6-0 IRanges_2.10.2
[22] S4Vectors_0.14.3 stats4_3.4.0 bit64_0.9-7
[25] grid_3.4.0 R6_2.2.2 AnnotationDbi_1.38.1 [28] tcltk_3.4.0 XML_3.98-1.9 survival_2.41-3
[31] polyclip_1.6-1 tensor_1.5 deldir_0.1-14
[34] blob_1.1.0 magrittr_1.5 MASS_7.3-47
[37] splines_3.4.0 abind_1.4-5 xtable_1.8-2
[40] RCurl_1.95-4.8 affyio_1.46.0

Anyone knows how I can resolve these errors?

Thanks in advance.

Regards,

Jianhai

ADD COMMENTlink modified 4 months ago by Jean-Karim Heriche13k • written 4 months ago by zhang.jianhai0
0
gravatar for Jean-Karim Heriche
4 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche13k wrote:

Read the error messages. They tell you what the problem is.

ADD COMMENTlink written 4 months ago by Jean-Karim Heriche13k
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