Dependency analysis on package lumi

General information

Bioconductor link link
Package version2.48.0
Number of strong dependencies162
Number of all dependencies170
Number of parent packages19
Max heaviness from parent packages53
Total heaviness from parent packages58
Number of parent packages (including Suggests and Enhances)27
Max co-heaviness from parent packages ("methylumi" and "GenomicFeatures")47

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of lumi and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on lumi.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests stats utils methods graphics grDevices stats4 tools grid splines parallel BiocGenerics zlibbioc Biobase rlang glue pkgconfig vctrs cli S4Vectors IRanges GenomeInfoDb RCurl GenomeInfoDbData XVector bitops Rcpp DBI bit64 blob memoise plogr bit cachem fastmap R6 crayon Biostrings httr RSQLite KEGGREST curl jsonlite mime openssl png askpass sys lattice Matrix AnnotationDbi nlme XML lifecycle digest tibble withr magrittr ellipsis fansi pillar utf8 preprocessCore xtable GenomicRanges stringr stringi scales ggplot2 farver labeling munsell RColorBrewer viridisLite gtable isoband MASS mgcv limma colorspace affyio BiocManager matrixStats SummarizedExperiment DelayedArray BiocParallel MatrixGenerics BiocIO rtracklayer biomaRt xml2 dplyr futile.logger snow codetools BH Rsamtools GenomicAlignments restfulr progress BiocFileCache rappdirs hms generics tidyselect purrr lambda.r futile.options Rhtslib rjson yaml prettyunits dbplyr filelock formatR assertthat reshape2 annotate illuminaio plyr org.Hs.eg.db survival base64 FDb.InfiniumMethylation.hg19 minfi genefilter GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene bumphunter beanplot nor1mix siggenes DelayedMatrixStats mclust reshape quadprog data.table GEOquery HDF5Array foreach iterators locfit doRNG multtest scrime sparseMatrixStats readr tidyr R.utils rhdf5 rhdf5filters Rhdf5lib rngtools clipr vroom cpp11 tzdb R.oo R.methodsS3 affy lumi methylumi nleqslv KernSmooth hexbin BeadDataPackR 0 20 40 Imported methods 0 50 100 150 Required packages 0 20 40 Heaviness from parents Biobase nleqslv graphics stats stats4 methods KernSmooth preprocessCore DBI lattice MASS mgcv affy GenomicRanges RSQLite AnnotationDbi annotate GenomicFeatures methylumi RColorBrewer limma vsn lumiHumanAll.db genefilter beadarray lumiBarnes lumiHumanIDMapping In total 162 packages are required directly or indirectly (170) when installing 'lumi' (2.48.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'lumi' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of lumi.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on lumi: number of required packages that can be reduced if moving parent package to Suggests of lumi.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on lumi
Biobase Depends 14 32 7 5 0
methylumi Imports 3 15 4 156 53
affy Imports 4 0 0 11 3
nleqslv Imports 1 0 0 0 1
KernSmooth Imports 1 0 0 1 1
graphics Imports 18 0 0 0 0
stats Imports 20 0 0 0 0
stats4 Imports 2 0 0 0 0
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of lumi. 0 0
preprocessCore Imports 2 0 0 1 0
DBI Imports 10 0 0 1 0
lattice Imports 2 0 0 5 0
MASS Imports 2 0 0 5 0
mgcv Imports 6 0 0 10 0
GenomicRanges Imports 1 0 0 15 0
RSQLite Imports 0 5 2 17 0
AnnotationDbi Imports 2 2 1 44 0
annotate Imports 2 0 0 47 0
GenomicFeatures Imports 1 0 0 96 0
beadarray Suggests No object is imported into the namespace of lumi. 81 3
lumiBarnes Suggests No object is imported into the namespace of lumi. 163 2
lumiHumanIDMapping Suggests No object is imported into the namespace of lumi. 163 2
vsn Suggests No object is imported into the namespace of lumi. 46 1
lumiHumanAll.db Suggests No object is imported into the namespace of lumi. 46 1
RColorBrewer Suggests No object is imported into the namespace of lumi. 0 0
limma Suggests No object is imported into the namespace of lumi. 5 0
genefilter Suggests No object is imported into the namespace of lumi. 53 0

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

Parent 1 Parent 2 Co-heaviness on lumi Co-heaviness as Jaccard coeffcient
GenomicFeatures methylumi 47 0.47

Analysis was done with pkgndep.