ScoreMatrixBin not working in version 1.35.0

[shuye2009]

I am trying to run your devel version (1.35.0) of genomation , but the ScoreMatrixBin function gives me an error (I have Matrix 1.7-0 installed):

library(genomation) data(cage) data(cpgi) data(promoters) myMat=ScoreMatrixBin(target=cage,

•                  windows=cpgi,bin.num=10,bin.op="mean",weight.col="tpm")
  

Error in validObject(.Object) : invalid class “ScoreMatrix” object: superclass "mMatrix" not defined in the environment of the object's class In addition: Warning message: In .local(target, windows, bin.num, bin.op, strand.aware) :

1 windows fall off the target

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.4.0 alpha (2024-03-26 r86209 ucrt) os Windows 10 x64 (build 19045) system x86_64, mingw32 ui RStudio language (EN) collate English_United States.utf8 ctype English_United States.utf8 tz America/New_York date 2024-03-29 rstudio 2023.12.0+369 Ocean Storm (desktop) pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)

How can I solve this problem?

Thanks a lot!

[shuye2009]

Is anyone looking into this issue? Here is the complete history of running the example for ScoreMatrixBin:

library(genomation) Loading required package: grid Warning message: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’

data(cage) data(cpgi) data(promoters) myMat=ScoreMatrixBin(target=cage, windows=cpgi,bin.num=10,bin.op="mean",weight.col="tpm")

Error in validObject(.Object) : invalid class “ScoreMatrix” object: superclass "mMatrix" not defined in the environment of the object's class In addition: Warning message: In .local(target, windows, bin.num, bin.op, strand.aware) : 1 windows fall off the target

sessionInfo()

R version 4.4.0 alpha (2024-03-26 r86209 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)
Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: America/New_York tzcode source: internal attached base packages: [1] grid stats graphics grDevices utils datasets methods base

other attached packages: [1] genomation_1.35.0

loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.33.3 gtable_0.3.4 impute_1.77.0 rjson_0.2.21
[5] ggplot2_3.5.0 Biobase_2.63.0 lattice_0.22-6 seqPattern_1.35.0
[9] tzdb_0.4.0 vctrs_0.6.5 tools_4.4.0 bitops_1.0-7
[13] generics_0.1.3 stats4_4.4.0 parallel_4.4.0 tibble_3.2.1
[17] fansi_1.0.6 pkgconfig_2.0.3 KernSmooth_2.23-22 Matrix_1.7-0
[21] data.table_1.15.2 BSgenome_1.71.3 S4Vectors_0.41.5 lifecycle_1.0.4
[25] GenomeInfoDbData_1.2.12 compiler_4.4.0 stringr_1.5.1 Rsamtools_2.19.4
[29] Biostrings_2.71.5 munsell_0.5.0 codetools_0.2-19 GenomeInfoDb_1.39.9
[33] RCurl_1.98-1.14 yaml_2.3.8 pillar_1.9.0 crayon_1.5.2
[37] BiocParallel_1.37.1 DelayedArray_0.29.9 abind_1.4-5 tidyselect_1.2.1
[41] stringi_1.8.3 dplyr_1.1.4 reshape2_1.4.4 restfulr_0.0.15
[45] colorspace_2.1-0 cli_3.6.2 SparseArray_1.3.4 magrittr_2.0.3
[49] S4Arrays_1.3.6 XML_3.99-0.16.1 utf8_1.2.4 readr_2.1.5
[53] scales_1.3.0 plotrix_3.8-4 XVector_0.43.1 httr_1.4.7
[57] matrixStats_1.2.0 hms_1.1.3 GenomicRanges_1.55.4 IRanges_2.37.1
[61] BiocIO_1.13.0 rtracklayer_1.63.1 rlang_1.1.3 Rcpp_1.0.12
[65] gridBase_0.4-7 glue_1.7.0 BiocGenerics_0.49.1 rstudioapi_0.16.0
[69] R6_2.5.1 plyr_1.8.9 MatrixGenerics_1.15.0 GenomicAlignments_1.39.5
[73] zlibbioc_1.49.3

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