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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