Dependency analysis on package lumiHumanIDMapping

General information

Bioconductor link link
Package version1.10.1
Number of strong dependencies163
Number of all dependencies163
Number of parent packages4
Max heaviness from parent packages118
Total heaviness from parent packages118
Number of parent packages (including Suggests and Enhances)4
Max co-heaviness from parent packages ("lumi" and "AnnotationDbi")43

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of lumiHumanIDMapping 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 lumiHumanIDMapping.

Adjust heatmap size:
Base packages Other packages Depends Imports methods graphics stats stats4 utils grDevices tools grid splines parallel Biobase RSQLite DBI BiocGenerics zlibbioc S4Vectors IRanges GenomeInfoDb RCurl XVector Biostrings httr bit64 blob memoise pkgconfig Rcpp plogr KEGGREST R6 rlang glue GenomeInfoDbData bitops crayon curl jsonlite mime openssl bit vctrs cachem png askpass cli fastmap sys affy methylumi GenomicFeatures GenomicRanges annotate lattice mgcv nleqslv KernSmooth preprocessCore AnnotationDbi MASS affyio BiocManager scales reshape2 ggplot2 matrixStats FDb.InfiniumMethylation.hg19 minfi SummarizedExperiment genefilter illuminaio BiocIO rtracklayer biomaRt XML xtable nlme Matrix farver labeling lifecycle munsell RColorBrewer viridisLite plyr stringr digest gtable isoband tibble withr TxDb.Hsapiens.UCSC.hg19.knownGene org.Hs.eg.db bumphunter beanplot nor1mix siggenes limma DelayedMatrixStats mclust reshape quadprog data.table GEOquery DelayedArray HDF5Array BiocParallel MatrixGenerics survival base64 Rsamtools GenomicAlignments restfulr progress BiocFileCache rappdirs xml2 colorspace magrittr stringi ellipsis fansi pillar foreach iterators locfit doRNG multtest scrime sparseMatrixStats readr dplyr tidyr R.utils rhdf5 rhdf5filters Rhdf5lib futile.logger snow codetools BH Rhtslib rjson yaml hms prettyunits dbplyr filelock utf8 rngtools clipr vroom cpp11 tzdb generics tidyselect purrr R.oo R.methodsS3 lambda.r futile.options assertthat formatR 0 1 2 3 Imported methods 0 50 100 150 Required packages 0 50 100 Heaviness from parents methods AnnotationDbi lumi DBI In total 163 packages are required directly or indirectly (163) when installing 'lumiHumanIDMapping' (1.10.1) Depends Imports Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'lumiHumanIDMapping' Imported S4 methods The whole namespace is imported


Dependency table

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

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 lumiHumanIDMapping: number of required packages that can be reduced if moving parent package to Suggests of lumiHumanIDMapping.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on lumiHumanIDMapping
lumi Depends The whole set of functions/methods/classes from parent package is imported to the namespace of lumiHumanIDMapping. 162 118
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of lumiHumanIDMapping. 0 0
AnnotationDbi Depends The whole set of functions/methods/classes from parent package is imported to the namespace of lumiHumanIDMapping. 44 0
DBI Imports 0 3 0 1 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 lumiHumanIDMapping Co-heaviness as Jaccard coeffcient
AnnotationDbi lumi 43 0.267

Analysis was done with pkgndep.