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-boun...@r-project.org on behalf of robert.cast...@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.
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--
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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