Error: not-yet-implemented method for cbind2(<try-error>, <dgCMatrix>).

[parvathisudha]

Hi,

I am running Mutspot for SNVs and Indels for one chromosome (chr2 of hg38).

I am getting an error after binning using mean_rep_time.

Error message:
[1] "./features/localmutrate_snv.bed"
Error: not-yet-implemented method for cbind2(, ).
->> Ask the package authors to implement the missing feature.
In addition: Warning messages:
1: In file.remove(nucleotide.selected.file) :
cannot remove file '/N/project/Walker_lab/WGS/Hotspot/Mutspot/Chr2/results/nucleotide_selected.RDS', reason 'No such file or directory'
2: In parallel::mclapply(1:nrow(continuous.features.urls), function(f) { :
scheduled core 1 encountered error in user code, all values of the job will be affected

Complete log:

MutSpot(snv.mutations = "WGS_99samples_chr2_snvs.MAF", indel.mutations = "WGS_99samples_chr2_indels.MAF",cores =12, cutoff.nucleotide.new = 1, genomic.features = "genomic_features_genome_default.txt")
[1] "Sample sites from SNV/indel"
[1] ">> Reading compact MAF ..."
[1] ">> Reading compact MAF ..."
[1] "Sampling to be done..."
[1] "Sampling SNV sites..."
[1] "Sampling indel sites..."
[1] "Calculate local mutation rates for SNV/indel"
[1] "Calculate local mutation rate for SNV..."
[1] ">> Reading compact MAF ..."
[1] ">> Reading compact MAF ..."
[1] "Select nucleotide context for SNV and filter polyAT from indel"
[1] "SNV mutations available..."
[1] "Progress : 1/100"
[1] "Progress : 2/100"
[1] "Progress : 3/100"
[1] "Progress : 4/100"
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[1][1] "Progress : 100/100"
"Progress : 99/100"
[1] "Progress : 97/100"
[1] "Indel mutations available..."
[1] ">> Reading compact MAF ..."
[1] ">> Reading compact MAF ..."
[1] "Reselect nucleotide context for SNV using altered threshold"
[1] "Select epigenetic features for SNV/indel"
[1] "Binning mean_rep_time into 10 bins"
[1] "/N/project/Walker_lab/WGS/Hotspot/Mutspot/Chr2/features/mean_rep_time.bed"
[1] "./features/localmutrate_snv.bed"
Error: not-yet-implemented method for cbind2(, ).
->> Ask the package authors to implement the missing feature.
In addition: Warning messages:
1: In file.remove(nucleotide.selected.file) :
cannot remove file '/N/project/Walker_lab/WGS/Hotspot/Mutspot/Chr2/results/nucleotide_selected.RDS', reason 'No such file or directory'
2: In parallel::mclapply(1:nrow(continuous.features.urls), function(f) { :
scheduled core 1 encountered error in user code, all values of the job will be affected

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS/LAPACK: /geode2/soft/hps/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_rt.so

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

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

other attached packages:
[1] poibin_1.5 stringi_1.6.2
[3] stringr_1.4.0 plyr_1.8.6
[5] glmnet_4.1-1 Matrix_1.3-3
[7] ggplot2_3.3.3 data.table_1.14.0
[9] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.54.0
[11] rtracklayer_1.46.0 GenomicRanges_1.38.0
[13] GenomeInfoDb_1.22.1 Biostrings_2.52.0
[15] XVector_0.24.0 IRanges_2.20.2
[17] S4Vectors_0.24.4 BiocGenerics_0.32.0
[19] MutSpot_0.0.0.9000

loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.16.1 shape_1.4.6
[3] tidyselect_1.1.1 purrr_0.3.4
[5] splines_3.6.0 lattice_0.20-44
[7] colorspace_2.0-1 vctrs_0.3.8
[9] generics_0.1.0 utf8_1.2.1
[11] XML_3.99-0.3 survival_3.2-11
[13] rlang_0.4.11 pillar_1.6.1
[15] glue_1.4.2 withr_2.4.2
[17] DBI_1.1.1 BiocParallel_1.20.1
[19] matrixStats_0.59.0 GenomeInfoDbData_1.2.2
[21] foreach_1.5.1 lifecycle_1.0.0
[23] zlibbioc_1.30.0 munsell_0.5.0
[25] gtable_0.3.0 codetools_0.2-18
[27] Biobase_2.44.0 fansi_0.4.2
[29] Rcpp_1.0.6 scales_1.1.1
[31] DelayedArray_0.12.3 Rsamtools_2.2.3
[33] dplyr_1.0.6 grid_3.6.0
[35] tools_3.6.0 bitops_1.0-7
[37] magrittr_2.0.1 RCurl_1.98-1.3
[39] tibble_3.1.2 crayon_1.4.1
[41] pkgconfig_2.0.3 ellipsis_0.3.2
[43] assertthat_0.2.1 iterators_1.0.13
[45] R6_2.5.0 GenomicAlignments_1.22.1
[47] compiler_3.6.0

Is there any version difference for any package I have loaded? I tried using the R library "methods", but getting the same error.
Can you please tell me how to solve this issue?

Thanks
Parvathi.