R session aborted when using adj2igraph() with the tutorial data and code.

[vicflonun]

Hello, I am running the tutorial for the -Analysis of American Gut data-. When I transform the adjacency matrices to the igraph object, the session aborts immediately. This happens only for the objects generated with the spiec.easi() function in:

ig.mb <- adj2igraph(getRefit(se.mb.amgut)) ig.gl <- adj2igraph(getRefit(se.gl.amgut))

but not for the object generated with the sparcc() function in

ig.sparcc <- adj2igraph(sparcc.graph)

The same problem occurs when I try to generate the igraph object using the igraph package, e.g.

library(igraph) ig.mb <- graph_from_adjacency_matrix(getRefit(se.mb.amgut), mode = "undirected", weighted = T)

I am not sure how to troubleshoot this, any insight to do so would be highly appreciated. Thanks

My sessionInfo()

R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

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

other attached packages: [1] SpiecEasi_1.1.3 Matrix_1.6-5

loaded via a namespace (and not attached): [1] Rcpp_1.0.12 ape_5.8 phyloseq_1.42.0 lattice_0.20-45 tidyr_1.3.1
[6] Biostrings_2.66.0 glmnet_4.1-8 digest_0.6.35 foreach_1.5.2 utf8_1.2.4
[11] R6_2.5.1 GenomeInfoDb_1.34.9 plyr_1.8.9 stats4_4.2.2 ggplot2_3.5.0
[16] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.3 microbiome_1.20.0 rstudioapi_0.16.0
[21] data.table_1.15.4 vegan_2.6-4 S4Vectors_0.36.2 splines_4.2.2 Rtsne_0.17
[26] stringr_1.5.1 igraph_2.0.3 RCurl_1.98-1.14 munsell_0.5.1 compiler_4.2.2
[31] pkgconfig_2.0.3 BiocGenerics_0.44.0 multtest_2.54.0 shape_1.4.6.1 mgcv_1.8-41
[36] biomformat_1.26.0 tidyselect_1.2.1 tibble_3.2.1 GenomeInfoDbData_1.2.9 IRanges_2.32.0
[41] codetools_0.2-19 fansi_1.0.6 permute_0.9-7 crayon_1.5.2 dplyr_1.1.4
[46] MASS_7.3-58.2 rhdf5filters_1.10.1 bitops_1.0-7 grid_4.2.2 nlme_3.1-162
[51] jsonlite_1.8.8 gtable_0.3.4 lifecycle_1.0.4 magrittr_2.0.3 scales_1.3.0
[56] huge_1.3.5 cli_3.6.2 stringi_1.8.3 pulsar_0.3.11 XVector_0.38.0
[61] reshape2_1.4.4 generics_0.1.3 vctrs_0.6.5 Rhdf5lib_1.20.0 iterators_1.0.14
[66] tools_4.2.2 ade4_1.7-22 Biobase_2.58.0 glue_1.7.0 purrr_1.0.2
[71] parallel_4.2.2 survival_3.4-0 colorspace_2.1-0 rhdf5_2.42.1 cluster_2.1.4
[76] VGAM_1.1-10

[zdk123]

I think there's an issue with Matrix v1.6-5. Thanks for reporting this.

[sunilnagpal]

Hello, Thanks for maintaining SpiecEasi! I am facing the same issue and wondering if this has some interim solution? Thanks again