I am unable to run the learn.bn function from Pigengene on my local windows system. I am reproducing the process outline in the PDF guide of pigengene.

The problem seem to be the sub-function which.cluster() which uses system("echo $HOSTNAME", intern = TRUE) which will not work on a windows os. using the r based sys.info() function instead might work, but I do not know how to make this change or find a github repository to submit a pull request. Is there a way to fix this?

See code and environment below.

learnt <- learn.bn(
  pigengene = pigengene,
  bnPath = file.path(saveDir, "bn"),
  bnNum = 10,
  seed = 1, 
  verbose = 4,
  onCluster = FALSE
)

learn.bn() with bnNum= 10 started at:
2024-12-13 14:24:37.574856
Start learning 10 BNs for module E using hc
moduleFile:
steps/bn/modE/moduleEH1.RData
Tracing system("echo $HOSTNAME", intern = TRUE) on entry 
[[1]]
learn.bn(pigengene = pigengene, bnPath = file.path(saveDir, "bn"), 
    bnNum = 10, seed = 1, verbose = 4, onCluster = FALSE)

[[2]]
bn.module(resultPath = bnPath, saveToPath = indvPath, moduleNum = moduleNum, 
    use.Hartemink = use.Hartemink, bnNum = bnNum, perJob = perJob, 
    use.Effect = use.Effect, use.Disease = use.Disease, dummies = dummies, 
    pertFrac = pertFrac, scoring = scoring, Data = Data, Labels = Labels, 
    bnStartFile = bnStartFile, selectedFeatures = selectedFeatures, 
    bnCalculationJob = bnCalculationJob, timeJob = timeJob, algo = algo, 
    seed = seed, verbose = verbose - 1, partition = NULL, maxSeconds = maxSeconds, 
    moduleFile = moduleFile, doShuffle = doShuffle, naTolerance = naTolerance)

[[3]]
which.cluster()

[[4]]
grep(x = system("echo $HOSTNAME", intern = TRUE), pattern = "stampede")

[[5]]
is.factor(x)

[[6]]
system("echo $HOSTNAME", intern = TRUE)

[[7]]
.doTrace(print(sys.calls()), "on entry")

[[8]]
eval.parent(exprObj)

[[9]]
eval(expr, p)

[[10]]
eval(expr, p)

Error in system("echo $HOSTNAME", intern = TRUE) : 'echo' not found


 sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: America/Indianapolis
tzcode source: internal

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

other attached packages:
[1] bnlearn_5.0.1       Pigengene_1.30.0    BiocStyle_2.32.1    graph_1.82.0        BiocGenerics_0.50.0

loaded via a namespace (and not attached):
  [1] libcoin_1.0-10          RColorBrewer_1.1-3      rstudioapi_0.17.1       jsonlite_1.8.9          magrittr_2.0.3         
  [6] farver_2.1.2            rmarkdown_2.29          fs_1.6.5                zlibbioc_1.50.0         vctrs_0.6.5            
 [11] memoise_2.0.1           base64enc_0.1-3         ggtree_3.12.0           htmltools_0.5.8.1       dynamicTreeCut_1.63-1  
 [16] gridGraphics_0.5-1      Formula_1.2-5           htmlwidgets_1.6.4       plyr_1.8.9              httr2_1.0.7            
 [21] impute_1.78.0           cachem_1.1.0            igraph_2.1.2            iterators_1.0.14        lifecycle_1.0.4        
 [26] pkgconfig_2.0.3         gson_0.1.0              Matrix_1.7-1            R6_2.5.1                fastmap_1.2.0          
 [31] GenomeInfoDbData_1.2.12 digest_0.6.37           aplot_0.2.3             enrichplot_1.24.4       colorspace_2.1-1       
 [36] patchwork_1.3.0         AnnotationDbi_1.66.0    S4Vectors_0.42.1        Hmisc_5.2-1             RSQLite_2.3.9          
 [41] fansi_1.0.6             gdata_3.0.1             httr_1.4.7              polyclip_1.10-7         compiler_4.4.2         
 [46] doParallel_1.0.17       bit64_4.5.2             withr_3.0.2             backports_1.5.0         htmlTable_2.4.3        
 [51] graphite_1.50.0         BiocParallel_1.38.0     viridis_0.6.5           DBI_1.2.3               ggforce_0.4.2          
 [56] R.utils_2.12.3          MASS_7.3-61             rappdirs_0.3.3          gtools_3.9.5            tools_4.4.2            
 [61] foreign_0.8-87          scatterpie_0.2.4        ape_5.8                 zip_2.3.1               nnet_7.3-19            
 [66] R.oo_1.27.0             glue_1.8.0              nlme_3.1-166            GOSemSim_2.30.2         inum_1.0-5             
 [71] shadowtext_0.1.4        grid_4.4.2              checkmate_2.3.2         cluster_2.1.6           Cubist_0.4.4           
 [76] reshape2_1.4.4          fgsea_1.30.0            generics_0.1.3          gtable_0.3.6            preprocessCore_1.66.0  
 [81] R.methodsS3_1.8.2       tidyr_1.3.1             WGCNA_1.73              data.table_1.16.4       tidygraph_1.3.1        
 [86] utf8_1.2.4              XVector_0.44.0          foreach_1.5.2           ggrepel_0.9.6           pillar_1.9.0           
 [91] stringr_1.5.1           yulab.utils_0.1.8       partykit_1.2-23         splines_4.4.2           dplyr_1.1.4            
 [96] tweenr_2.0.3            treeio_1.28.0           lattice_0.22-6          survival_3.7-0          bit_4.5.0.1            
[101] tidyselect_1.2.1        GO.db_3.19.1            Biostrings_2.72.1       reactome.db_1.88.0      knitr_1.49             
[106] gridExtra_2.3           C50_0.1.8               IRanges_2.38.1          stats4_4.4.2            xfun_0.49              
[111] graphlayouts_1.2.1      Biobase_2.64.0          matrixStats_1.4.1       pheatmap_1.0.12         stringi_1.8.4          
[116] UCSC.utils_1.0.0        lazyeval_0.2.2          ggfun_0.1.8             yaml_2.3.10             ReactomePA_1.48.0      
[121] evaluate_1.0.1          codetools_0.2-20        ggraph_2.2.1            tibble_3.2.1            qvalue_2.36.0          
[126] Rgraphviz_2.48.0        BiocManager_1.30.25     ggplotify_0.1.2         cli_3.6.3               rpart_4.1.23           
[131] munsell_0.5.1           Rcpp_1.0.13-1           GenomeInfoDb_1.40.1     png_0.1-8               fastcluster_1.2.6      
[136] parallel_4.4.2          ggplot2_3.5.1           blob_1.2.4              clusterProfiler_4.12.6  DOSE_3.30.5            
[141] tidytree_0.4.6          viridisLite_0.4.2       mvtnorm_1.3-2           scales_1.3.0            openxlsx_4.2.7.1       
[146] purrr_1.0.2             crayon_1.5.3            rlang_1.1.4             cowplot_1.1.3           fastmatch_1.1-4        
[151] KEGGREST_1.44.1

Any help will be greatly appreciated!