makeBSseqData problem versions
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@bernadetterubio-23833
Last seen 14 months ago

Hi,

I use the DSS package to identify DMRs. I has already written a script that worked very well with the first data that I had tested. I wanted to reuse this same script but now I am blocked when using the function "makeBSseqData". I get the following error :

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'normalize_names_replacement_value' not found
Calls: makeBSseqData ... new_GRanges -> IRanges -> names<- -> names<- -> ::: -> get
Execution halted

After some reseach, I have the impression that the problem could be in connection with updates of S4vector but I cannot resolve the problem.

Could someone give me some leads to test ?

Thanks in advance,

Bernadette

SessionInfo()

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /tools/R/R-3.6.2/lib64/R/lib/libRblas.so
LAPACK: /tools/R/R-3.6.2/lib64/R/lib/libRlapack.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] splines   stats4    parallel  stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
 [1] DSS_2.34.0                  bsseq_1.22.0
 [3] SummarizedExperiment_1.14.1 DelayedArray_0.12.2
 [5] BiocParallel_1.18.1         matrixStats_0.56.0
 [7] GenomicRanges_1.36.1        GenomeInfoDb_1.22.1
 [9] IRanges_2.18.2              S4Vectors_0.24.3
[11] Biobase_2.46.0              BiocGenerics_0.32.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4               BiocManager_1.30.10      compiler_3.6.2
 [4] XVector_0.26.0           R.methodsS3_1.8.0        R.utils_2.9.2
 [7] bitops_1.0-6             tools_3.6.2              DelayedMatrixStats_1.8.0
[10] zlibbioc_1.32.0          lifecycle_0.2.0          rhdf5_2.30.1
[13] lattice_0.20-38          BSgenome_1.54.0          rlang_0.4.5
[16] Matrix_1.2-18            GenomeInfoDbData_1.2.2   rtracklayer_1.44.3
[19] Biostrings_2.54.0        gtools_3.8.2             locfit_1.5-9.4
[22] grid_3.6.2               data.table_1.12.2        R6_2.4.1
[25] HDF5Array_1.14.3         XML_3.99-0.3             limma_3.42.2
[28] Rhdf5lib_1.8.0           GenomicAlignments_1.20.1 scales_1.1.1
[31] Rsamtools_2.2.3          permute_0.9-5            colorspace_1.4-1
[34] RCurl_1.98-1.2           munsell_0.5.0            R.oo_1.23.0
software error • 142 views
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