I'm coming across a problem while trying to analyze WGBS data from CD4 and CD8 T cells (3 vs 3 samples). I used the following code:
bsseq_obj = BSseq(chr = chr, pos = position, M = M, Cov = C, sampleNames = sample_names)
replicate = c(seq(1,length(group1_sample_list)), seq(1,length(group2_sample_list)))
bsseq::pData(bsseq_obj) = data.frame(row.names = sample_names, replicate, tissue)
bsseq_obj = renameSeqlevels(bsseq_obj, mapSeqlevels(seqlevels(bsseq_obj), "UCSC"))
bsseq_obj = bsseq_obj[seqnames(bsseq_obj)=="chr19",]
bs.fit = BSmooth(bsseq_obj)
For testing purposes, I am only focusing on chr 19 with 1057376 CpG sites in total.
The error appears after calling BSmooth:
Error in env[[as.character(i)]] <- value :
wrong args for environment subassignment
In addition: Warning message:
In parallel::mccollect(wait = FALSE, timeout = 1) :
1 parallel job did not deliver a result
BiocManager::valid() returns TRUE.
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] HDF5Array_1.22.1 rhdf5_2.38.1 DelayedArray_0.20.0 Matrix_1.4-1 bsseq_1.30.0
[6] SummarizedExperiment_1.24.0 Biobase_2.54.0 MatrixGenerics_1.6.0 matrixStats_0.61.0 GenomicRanges_1.46.1
[11] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 ExperimentHub_2.2.1 AnnotationHub_3.2.2
[16] BiocFileCache_2.2.1 dbplyr_2.1.1 BiocGenerics_0.40.0 DMRcate_2.8.5
loaded via a namespace (and not attached):
[1] utf8_1.2.2 R.utils_2.11.0
[3] tidyselect_1.1.2 RSQLite_2.2.12
[5] AnnotationDbi_1.56.2 htmlwidgets_1.5.4
[7] grid_4.1.3 BiocParallel_1.28.3
[9] munsell_0.5.0 codetools_0.2-18
[11] preprocessCore_1.56.0 statmod_1.4.36
[13] colorspace_2.0-3 filelock_1.0.2
[15] knitr_1.38 rstudioapi_0.13
[17] GenomeInfoDbData_1.2.7 bit64_4.0.5
[19] vctrs_0.4.0 generics_0.1.2
[21] xfun_0.30 biovizBase_1.42.0
[23] R6_2.5.1 illuminaio_0.36.0
[25] locfit_1.5-9.5 AnnotationFilter_1.18.0
[27] bitops_1.0-7 rhdf5filters_1.6.0
[29] cachem_1.0.6 reshape_0.8.8
[31] assertthat_0.2.1 promises_1.2.0.1
[33] BiocIO_1.4.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[35] scales_1.1.1 nnet_7.3-17
[37] gtable_0.3.0 ensembldb_2.18.4
[39] rlang_1.0.2 genefilter_1.76.0
[41] splines_4.1.3 rtracklayer_1.54.0
[43] lazyeval_0.2.2 DSS_2.42.0
[45] GEOquery_2.62.2 dichromat_2.0-0
[47] checkmate_2.0.0 BiocManager_1.30.16
[49] yaml_2.3.5 GenomicFeatures_1.46.5
[51] backports_1.4.1 httpuv_1.6.5
[53] Hmisc_4.6-0 tools_4.1.3
[55] nor1mix_1.3-0 ggplot2_3.3.5
[57] ellipsis_0.3.2 RColorBrewer_1.1-3
[59] siggenes_1.68.0 Rcpp_1.0.8.3
[61] plyr_1.8.7 base64enc_0.1-3
[63] sparseMatrixStats_1.6.0 progress_1.2.2
[65] zlibbioc_1.40.0 purrr_0.3.4
[67] RCurl_1.98-1.6 prettyunits_1.1.1
[69] rpart_4.1.16 openssl_2.0.0
[71] bumphunter_1.36.0 cluster_2.1.3
[73] magrittr_2.0.3 data.table_1.14.2
[75] ProtGenerics_1.26.0 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[77] missMethyl_1.28.0 hms_1.1.1
[79] mime_0.12 xtable_1.8-4
[81] XML_3.99-0.9 jpeg_0.1-9
[83] mclust_5.4.9 gridExtra_2.3
[85] compiler_4.1.3 biomaRt_2.50.3
[87] minfi_1.40.0 tibble_3.1.6
[89] crayon_1.5.1 R.oo_1.24.0
[91] htmltools_0.5.2 later_1.3.0
[93] tzdb_0.3.0 Formula_1.2-4
[95] tidyr_1.2.0 DBI_1.1.2
[97] MASS_7.3-56 rappdirs_0.3.3
[99] readr_2.1.2 permute_0.9-7
[101] cli_3.2.0 quadprog_1.5-8
[103] R.methodsS3_1.8.1 parallel_4.1.3
[105] Gviz_1.38.3 pkgconfig_2.0.3
[107] GenomicAlignments_1.30.0 foreign_0.8-82
[109] xml2_1.3.3 foreach_1.5.2
[111] annotate_1.72.0 rngtools_1.5.2
[113] multtest_2.50.0 beanplot_1.2
[115] XVector_0.34.0 doRNG_1.8.2
[117] scrime_1.3.5 stringr_1.4.0
[119] VariantAnnotation_1.40.0 digest_0.6.29
[121] Biostrings_2.62.0 base64_2.0
[123] htmlTable_2.4.0 edgeR_3.36.0
[125] DelayedMatrixStats_1.16.0 restfulr_0.0.13
[127] curl_4.3.2 shiny_1.7.1
[129] Rsamtools_2.10.0 gtools_3.9.2
[131] rjson_0.2.21 lifecycle_1.0.1
[133] nlme_3.1-157 Rhdf5lib_1.16.0
[135] askpass_1.1 limma_3.50.1
[137] BSgenome_1.62.0 fansi_1.0.3
[139] pillar_1.7.0 lattice_0.20-45
[141] KEGGREST_1.34.0 fastmap_1.1.0
[143] httr_1.4.2 survival_3.3-1
[145] interactiveDisplayBase_1.32.0 glue_1.6.2
[147] png_0.1-7 iterators_1.0.14
[149] BiocVersion_3.14.0 bit_4.0.4
[151] stringi_1.7.6 blob_1.2.2
[153] org.Hs.eg.db_3.14.0 latticeExtra_0.6-29
[155] memoise_2.0.1 dplyr_1.0.8
Thank you very much for your time.
I'm coming across a problem while trying to analyze WGBS data from CD4 and CD8 T cells (3 vs 3 samples). I used the following code:
For testing purposes, I am only focusing on chr 19 with 1057376 CpG sites in total.
The error appears after calling BSmooth:
BiocManager::valid()returns TRUE.Thank you very much for your time.