[Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

Robert Castelo robert@c@@te|o @end|ng |rom up|@edu
Thu Feb 6 12:36:08 CET 2020


when i load the package 'GenomicScores' in a clean session i see thorugh 
the 'sessionInfo()' that the package 'Matrix' is listed under "loaded 
via a namespace (and not attached)".

i'd like to know what is the dependency that 'GenomicsScores' has that 
ends up requiring the package 'Matrix'.

i've tried using the package 'pkgDepTools' without success, because the 
dependency graph does not list any path from 'GenomicScores' to 'Matrix'.

i've been manually browsing the Bioc website and, unless i've overlooked 
something, the only association with 'Matrix' i could find is that 
'S4Vectors' and 'GenomicRanges', which are required by 'GenomicScores', 
list 'Matrix' in the 'Suggests' field, but my understanding is that 
those packages are not required and should not be loaded.

so, is there any way in which i can figure out what of the 
'GenomicScores' dependencies leads to loading the package 'Matrix'?

here are the depends, import and suggests fields from 'GenomicScores':

Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods,
         BiocGenerics (>= 0.13.8)
Imports: utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings,
         BSgenome, GenomeInfoDb, AnnotationHub, shiny, shinyjs,
	DT, shinycustomloader, rtracklayer, data.table, shinythemes
Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
         phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5,
         SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation,
         TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer

and here a session information in a fresh R-devel session after loading 
the package 'GenomicScores':

R Under development (unstable) (2020-01-29 r77745)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /opt/R/R-devel/lib64/R/lib/libRblas.so
LAPACK: /opt/R/R-devel/lib64/R/lib/libRlapack.so

  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C

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

other attached packages:
[1] GenomicScores_1.11.4 GenomicRanges_1.39.2 GenomeInfoDb_1.23.10
[4] IRanges_2.21.3       S4Vectors_0.25.12    BiocGenerics_0.33.0
[7] colorout_1.2-2

loaded via a namespace (and not attached):
  [1] Rcpp_1.0.3                    lattice_0.20-38
  [3] shinycustomloader_0.9.0       Rsamtools_2.3.3
  [5] Biostrings_2.55.4             assertthat_0.2.1
  [7] digest_0.6.23                 mime_0.9
  [9] BiocFileCache_1.11.4          R6_2.4.1
[11] RSQLite_2.2.0                 httr_1.4.1
[13] pillar_1.4.3                  zlibbioc_1.33.1
[15] rlang_0.4.4                   curl_4.3
[17] data.table_1.12.8             blob_1.2.1
[19] DT_0.12                       Matrix_1.2-18
[21] shinythemes_1.1.2             shinyjs_1.1
[23] BiocParallel_1.21.2           AnnotationHub_2.19.7
[25] htmlwidgets_1.5.1             RCurl_1.98-1.1
[27] bit_1.1-15.1                  shiny_1.4.0
[29] DelayedArray_0.13.3           compiler_4.0.0
[31] httpuv_1.5.2                  rtracklayer_1.47.0
[33] pkgconfig_2.0.3               htmltools_0.4.0
[35] tidyselect_1.0.0              SummarizedExperiment_1.17.1
[37] tibble_2.1.3                  GenomeInfoDbData_1.2.2
[39] interactiveDisplayBase_1.25.0 matrixStats_0.55.0
[41] XML_3.99-0.3                  crayon_1.3.4
[43] dplyr_0.8.4                   dbplyr_1.4.2
[45] later_1.0.0                   GenomicAlignments_1.23.1
[47] bitops_1.0-6                  rappdirs_0.3.1
[49] grid_4.0.0                    xtable_1.8-4
[51] DBI_1.1.0                     magrittr_1.5
[53] XVector_0.27.0                promises_1.1.0
[55] vctrs_0.2.2                   tools_4.0.0
[57] bit64_0.9-7                   BSgenome_1.55.3
[59] Biobase_2.47.2                glue_1.3.1
[61] purrr_0.3.3                   BiocVersion_3.11.1
[63] fastmap_1.0.1                 yaml_2.2.1
[65] AnnotationDbi_1.49.1          BiocManager_1.30.10
[67] memoise_1.1.0



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