getLinkList fails to retrieve links

[philmaweb]

After calculating a weight matrix from gene expression matrix according to vignette instruction, filtering of links by threshold fails.

> dim(cnts)
[1] 55421    48

>exprMatr <- as.matrix(cnts)
>weightMat <- GENIE3(exprMatr, nCores=20, verbose=TRUE)
Tree method: RF
K: sqrt
Number of trees: 1000

Using 20 cores.

> dim(weightMat)
[1] 55421 55421
> linkList01 <- getLinkList(weightMat, threshold=0.001)
Error in if (n > 0) c(NA_integer_, -n) else integer() :
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In rep.fac * nx : NAs produced by integer overflow
2: In .set_row_names(as.integer(prod(d))) :
  NAs introduced by coercion to integer range

Initially GENIE3 refused to run with several cores, as it depends on "doParallel" "foreach" and "doRNG", which were not installed during setup. GENIE3 was installed using BiocManager::install("GENIE3"). After fixing the dependencies I can run the functions, but it seems like it can't handle the size of the matrix. Suggestions?

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS/LAPACK: /nfs/home/users/pweber/.conda/envs/genie3/lib/libopenblasp-r0.3.10.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] 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
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] doRNG_1.8.2                 rngtools_1.5
 [3] foreach_1.5.0               dplyr_1.0.0
 [5] GENIE3_1.10.0               DESeq2_1.28.1
 [7] SummarizedExperiment_1.18.1 DelayedArray_0.14.0
 [9] matrixStats_0.56.0          Biobase_2.48.0
[11] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2
[13] IRanges_2.22.2              S4Vectors_0.26.1
[15] BiocGenerics_0.34.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6           locfit_1.5-9.4         lattice_0.20-41
 [4] assertthat_0.2.1       digest_0.6.25          plyr_1.8.6
 [7] R6_2.4.1               RSQLite_2.2.0          ggplot2_3.3.2
[10] pillar_1.4.4           zlibbioc_1.34.0        rlang_0.4.6
[13] annotate_1.66.0        blob_1.2.1             Matrix_1.2-18
[16] splines_4.0.2          BiocParallel_1.22.0    stringr_1.4.0
[19] geneplotter_1.66.0     RCurl_1.98-1.2         bit_1.1-15.2
[22] munsell_0.5.0          compiler_4.0.2         pkgconfig_2.0.3
[25] tidyselect_1.1.0       tibble_3.0.1           GenomeInfoDbData_1.2.3
[28] codetools_0.2-16       XML_3.99-0.4           fansi_0.4.1
[31] crayon_1.3.4           bitops_1.0-6           grid_4.0.2
[34] xtable_1.8-4           gtable_0.3.0           lifecycle_0.2.0
[37] DBI_1.1.0              magrittr_1.5           scales_1.1.1
[40] stringi_1.4.6          cli_2.0.2              reshape2_1.4.4
[43] XVector_0.28.0         genefilter_1.70.0      doParallel_1.0.15
[46] ellipsis_0.3.1         generics_0.0.2         vctrs_0.3.1
[49] RColorBrewer_1.1-2     iterators_1.0.12       tools_4.0.2
[52] bit64_0.9-7            glue_1.4.1             purrr_0.3.4
[55] survival_3.2-3         AnnotationDbi_1.50.1   colorspace_1.4-1
[58] BiocManager_1.30.10    memoise_1.1.0