Entering edit mode
Hello All,
I am trying to run a model with variancePartition, which uses BiocParallel for parallel processing, on a Windows computer. I have run this program on my MacBook pro several times without any parallel processing issues. However, every time I run it on my partner's Windows computer, I am met with warnings and the model immediately quits. I would like to be able to run this on the Windows computer as it has more cores available than my Mac. I would opt to run it without parallel processing, but this takes far too much time, as when I tried it previously the model ran for more than 36 hours before it was interrupted by an automatic Windows update. I have googled this issue and tried some of the remedies suggested (e.g., restarting R, reducing the number of cores being used), but so far nothing has worked. I have included some of the code, the error/output, and the sessionInfo() below.
Code:
param <- SnowParam(workers= 8, "SOCK", progressbar = TRUE)
betafit.age <- dream(ilogit2(adj.m_matrix), formula, pheno, ddf = "Kenward-Roger", BPPARAM = param)
Output:
Error in serialize(data, node$con) : error writing to connection
iteration: Error in serialize(data, node$con) :
(converted from warning) 'package:stats' may not be available when loading
Error in serialize(data, node$con) : error writing to connection
> sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.utf8 LC_CTYPE=English_Canada.utf8
[3] LC_MONETARY=English_Canada.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Canada.utf8
time zone: America/Toronto
tzcode source: internal
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] dbplyr_2.4.0 variancePartition_1.32.2 BiocParallel_1.36.0
[4] limma_3.58.1 ggplot2_3.4.4 DMRcate_2.16.1
[7] minfi_1.48.0 bumphunter_1.44.0 locfit_1.5-9.8
[10] iterators_1.0.14 foreach_1.5.2 Biostrings_2.70.1
[13] XVector_0.42.0 SummarizedExperiment_1.32.0 Biobase_2.62.0
[16] MatrixGenerics_1.14.0 matrixStats_1.1.0 GenomicRanges_1.54.1
[19] GenomeInfoDb_1.38.1 IRanges_2.36.0 S4Vectors_0.40.2
[22] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] ProtGenerics_1.34.0
[2] fs_1.6.3
[3] bitops_1.0-7
[4] devtools_2.4.5
[5] httr_1.4.7
[6] RColorBrewer_1.1-3
[7] numDeriv_2016.8-1.1
[8] profvis_0.3.8
[9] tools_4.3.2
[10] doRNG_1.8.6
[11] backports_1.4.1
[12] utf8_1.2.4
[13] R6_2.5.1
[14] HDF5Array_1.30.0
[15] lazyeval_0.2.2
[16] Gviz_1.46.1
[17] permute_0.9-7
[18] rhdf5filters_1.14.1
[19] withr_2.5.2
[20] urlchecker_1.0.1
[21] prettyunits_1.2.0
[22] gridExtra_2.3
[23] base64_2.0.1
[24] preprocessCore_1.64.0
[25] cli_3.6.1
[26] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[27] mvtnorm_1.2-4
[28] readr_2.1.4
[29] genefilter_1.84.0
[30] askpass_1.2.0
[31] Rsamtools_2.18.0
[32] foreign_0.8-86
[33] R.utils_2.12.3
[34] siggenes_1.76.0
[35] illuminaio_0.44.0
[36] dichromat_2.0-0.1
[37] sessioninfo_1.2.2
[38] scrime_1.3.5
[39] BSgenome_1.70.1
[40] rstudioapi_0.15.0
[41] RSQLite_2.3.4
[42] generics_0.1.3
[43] BiocIO_1.12.0
[44] gtools_3.9.5
[45] dplyr_1.1.4
[46] interp_1.1-5
[47] Matrix_1.6-4
[48] fansi_1.0.6
[49] abind_1.4-5
[50] R.methodsS3_1.8.2
[51] lifecycle_1.0.4
[52] edgeR_4.0.3
[53] yaml_2.3.7
[54] gplots_3.1.3
[55] rhdf5_2.46.1
[56] SparseArray_1.2.2
[57] BiocFileCache_2.10.1
[58] grid_4.3.2
[59] blob_1.2.4
[60] promises_1.2.1
[61] ExperimentHub_2.10.0
[62] crayon_1.5.2
[63] miniUI_0.1.1.1
[64] lattice_0.21-9
[65] GenomicFeatures_1.54.1
[66] annotate_1.80.0
[67] KEGGREST_1.42.0
[68] pillar_1.9.0
[69] knitr_1.45
[70] beanplot_1.3.1
[71] rjson_0.2.21
[72] boot_1.3-28.1
[73] corpcor_1.6.10
[74] codetools_0.2-19
[75] glue_1.6.2
[76] data.table_1.14.10
[77] remotes_2.4.2.1
[78] vctrs_0.6.5
[79] png_0.1-8
[80] Rdpack_2.6
[81] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
[82] gtable_0.3.4
[83] cachem_1.0.8
[84] xfun_0.41
[85] rbibutils_2.2.16
[86] S4Arrays_1.2.0
[87] mime_0.12
[88] survival_3.5-7
[89] statmod_1.5.0
[90] interactiveDisplayBase_1.40.0
[91] ellipsis_0.3.2
[92] nlme_3.1-164
[93] pbkrtest_0.5.2
[94] usethis_2.2.2
[95] bit64_4.0.5
[96] bsseq_1.38.0
[97] progress_1.2.3
[98] EnvStats_2.8.1
[99] filelock_1.0.2
[100] nor1mix_1.3-2
[101] KernSmooth_2.23-22
[102] rpart_4.1.23
[103] colorspace_2.1-0
[104] DBI_1.1.3
[105] Hmisc_5.1-1
[106] nnet_7.3-19
[107] tidyselect_1.2.0
[108] bit_4.0.5
[109] compiler_4.3.2
[110] curl_5.2.0
[111] htmlTable_2.4.2
[112] xml2_1.3.6
[113] DelayedArray_0.28.0
[114] rtracklayer_1.62.0
[115] checkmate_2.3.1
[116] scales_1.3.0
[117] caTools_1.18.2
[118] remaCor_0.0.16
[119] quadprog_1.5-8
[120] rappdirs_0.3.3
[121] stringr_1.5.1
[122] digest_0.6.33
[123] minqa_1.2.6
[124] rmarkdown_2.25
[125] GEOquery_2.70.0
[126] aod_1.3.3
[127] RhpcBLASctl_0.23-42
[128] jpeg_0.1-10
[129] htmltools_0.5.7
[130] pkgconfig_2.0.3
[131] base64enc_0.1-3
[132] lme4_1.1-35.1
[133] sparseMatrixStats_1.14.0
[134] ensembldb_2.26.0
[135] fastmap_1.1.1
[136] rlang_1.1.2
[137] htmlwidgets_1.6.4
[138] shiny_1.8.0
[139] DelayedMatrixStats_1.24.0
[140] mclust_6.0.1
[141] R.oo_1.25.0
[142] VariantAnnotation_1.48.1
[143] RCurl_1.98-1.13
[144] magrittr_2.0.3
[145] Formula_1.2-5
[146] GenomeInfoDbData_1.2.11
[147] Rhdf5lib_1.24.1
[148] munsell_0.5.0
[149] Rcpp_1.0.11
[150] stringi_1.8.2
[151] zlibbioc_1.48.0
[152] MASS_7.3-60
[153] org.Hs.eg.db_3.18.0
[154] AnnotationHub_3.10.0
[155] plyr_1.8.9
[156] pkgbuild_1.4.3
[157] deldir_2.0-2
[158] splines_4.3.2
[159] multtest_2.58.0
[160] hms_1.1.3
[161] rngtools_1.5.2
[162] reshape2_1.4.4
[163] biomaRt_2.58.0
[164] pkgload_1.3.3
[165] missMethyl_1.36.0
[166] BiocVersion_3.18.1
[167] XML_3.99-0.16
[168] evaluate_0.23
[169] latticeExtra_0.6-30
[170] biovizBase_1.50.0
[171] BiocManager_1.30.22
[172] nloptr_2.0.3
[173] tzdb_0.4.0
[174] httpuv_1.6.13
[175] tidyr_1.3.0
[176] openssl_2.1.1
[177] purrr_1.0.2
[178] reshape_0.8.9
[179] broom_1.0.5
[180] xtable_1.8-4
[181] restfulr_0.0.15
[182] AnnotationFilter_1.26.0
[183] fANCOVA_0.6-1
[184] later_1.3.2
[185] snow_0.4-4
[186] tibble_3.2.1
[187] lmerTest_3.1-3
[188] memoise_2.0.1
[189] AnnotationDbi_1.64.1
[190] GenomicAlignments_1.38.0
[191] cluster_2.1.6
Can you provide a small example of the code that produces the error? It doesn't need to be with the full data set, but providing a little example that others can read and then copy/paste to test will probably get your more responses.
Thank you for the suggestion! I have edited my post to include some of the code I used.