[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 18:29:18 CET 2020
true, i was just searching for the shortest path, we can search for all
simple (i.e., without repeating "vertices") paths and there are up to
five routes from "GenomicScores" to "Matrix"
igraph::all_simple_paths(igraph::igraph.from.graphNEL(g),
from="GenomicScores", to="Matrix", mode="out")
[[1]]
+ 7/117 vertices, named, from 04133ec:
[1] GenomicScores BSgenome rtracklayer
[4] GenomicAlignments SummarizedExperiment DelayedArray
[7] Matrix
[[2]]
+ 6/117 vertices, named, from 04133ec:
[1] GenomicScores BSgenome rtracklayer
[4] GenomicAlignments SummarizedExperiment Matrix
[[3]]
+ 6/117 vertices, named, from 04133ec:
[1] GenomicScores DT crosstalk ggplot2 mgcv
[6] Matrix
[[4]]
+ 6/117 vertices, named, from 04133ec:
[1] GenomicScores rtracklayer GenomicAlignments
[4] SummarizedExperiment DelayedArray Matrix
[[5]]
+ 5/117 vertices, named, from 04133ec:
[1] GenomicScores rtracklayer GenomicAlignments
[4] SummarizedExperiment Matrix
this is interesting, because it means that if i wanted to get rid of the
"Matrix" dependence i'd need to get rid not only of the "rtracklayer"
dependence but also of "BSgenome" and "DT".
robert.
On 2/6/20 5:41 PM, Martin Morgan wrote:
> Excellent! I think there are other, independent, paths between your immediate dependents...
>
> RBGL::sp.between(g, start="DT", finish="Matrix", detail=TRUE)[[1]]$path_detail
> [1] "DT" "crosstalk" "ggplot2" "mgcv" "Matrix"
>
> ??
>
> Martin
>
> On 2/6/20, 10:47 AM, "Robert Castelo" <robert.castelo using upf.edu> wrote:
>
> hi Martin,
>
> thanks for hint!! i wasn't aware of 'tools::package_dependencies()',
> adding a bit of graph sorcery i get the result i was looking for:
>
> repos <- BiocManager::repositories()[c(1,5)]
> repos
> BioCsoft
> "https://bioconductor.org/packages/3.11/bioc"
> CRAN
> "https://cran.rstudio.com"
>
> db <- available.packages(repos=repos)
>
> deps <- tools::package_dependencies("GenomicScores", db,
> recursive=TRUE)[[1]]
>
> deps <- tools::package_dependencies(c("GenomicScores", deps), db)
>
> g <- graph::graphNEL(nodes=names(deps), edgeL=deps, edgemode="directed")
>
> RBGL::sp.between(g, start="GenomicScores", finish="Matrix",
> detail=TRUE)[[1]]$path_detail
> [1] "GenomicScores" "rtracklayer" "GenomicAlignments"
> [4] "SummarizedExperiment" "Matrix"
>
> so, it was the rtracklayer dependency that leads to Matrix through
> GenomeAlignments and SummarizedExperiment.
>
> maybe the BioC package 'pkgDepTools' should be deprecated if its
> functionality is part of 'tools' and it does not even work as fast and
> correct as 'tools'.
>
> cheers,
>
> robert.
>
>
> On 2/6/20 2:51 PM, Martin Morgan wrote:
> > 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:
> >
> > hi,
> >
> > 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
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
> > [3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
> > [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
> > [7] LC_PAPER=en_US.UTF8 LC_NAME=C
> > [9] LC_ADDRESS=C LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=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
> >
> >
> >
> > thanks!!
> >
> > robert.
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
>
>
--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550
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