Hi All. I'm having a problem while running BSmooth in the bsseq package. I have 25 WGBS samples, human, which I've processed using Bismark, and I have read the coverage files using read.bismark. However, when I try to run BSmooth, I get the following error:
> Meth.cov.fit <- BSmooth(Meth.cov, mc.cores = 32, verbose = TRUE) [BSmooth] preprocessing ... done in 37.1 sec [BSmooth] smoothing by 'sample' (mc.cores = 32, mc.preschedule = FALSE) [BSmooth] smoothing done in 17656.1 sec Error in names(object) <- nm : 'names' attribute  must be the same length as the vector 
Here is the session info:
> sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.8 (Final)` Matrix products: default BLAS/LAPACK: /usr/local/OpenBLAS/0.2.19/gcc-4.9.1/lib/libopenblas_nehalemp-r0.2.19.so` `locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=C  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C ` `attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base ` `other attached packages:  bsseq_1.12.2 SummarizedExperiment_1.6.5 DelayedArray_0.2.7 matrixStats_0.52.2  Biobase_2.36.2 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.5  S4Vectors_0.14.7 BiocGenerics_0.22.1 ` `loaded via a namespace (and not attached):  Rcpp_0.12.13 XVector_0.16.0 zlibbioc_1.22.0 munsell_0.4.3 colorspace_1.3-2  lattice_0.20-35 plyr_1.8.4 tools_3.4.0 grid_3.4.0 data.table_1.10.4-2  R.oo_1.21.0 gtools_3.5.0 permute_0.9-4 Matrix_1.2-11 GenomeInfoDbData_0.99.0  R.utils_2.5.0 bitops_1.0-6 RCurl_1.95-4.8 limma_3.33.13 compiler_3.4.0  R.methodsS3_1.7.1 scales_0.5.0 locfit_1.5-9.1
I am running R on a Linux cluster but using Rstudio through Xming, if that helps. Any help would be really appreciated, I'm quite puzzled by this.