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

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Feb 6 14:51:37 CET 2020

The first thing is to get the correct repositories

  repos = BiocManager::repositories()

(maybe trim the experiment and annotation repos from this). I also tried pkgDepTools::makeDepGraph() but it took so long that I moved on... it has an option 'keep.builtin' which might include Matrix.

There is also BiocPkgTools::buildPkgDependencyDataFrame() & friends, but this seems to build dependencies within a single repository...

The building block for a solution is `tools::package_dependencies()`, and I can confirm that "Matrix" _is_ a dependency

  db = available.packages(repos = BiocManager::repositories())
  revdeps <- tools::package_dependencies("GenomicScores", db, recursive = TRUE)
  "Matrix" %in% revdeps[[1]]
  ## [1] TRUE

so I'll leave the clever recursive or graph-based algorithm up to you, to report back to the mailing list?

For what it's worth I think the last time this came up Martin Maechler pointed to a function in base R (probably the tools package) that implements this, too...?

Martin Morgan

On 2/6/20, 6:40 AM, "Bioc-devel on behalf of Robert Castelo" <bioc-devel-bounces using r-project.org on behalf of robert.castelo using upf.edu> wrote:

    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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