Dependency analysis on package lumiBarnes

General information

Bioconductor link link
Package version1.36.0
Number of strong dependencies163
Number of all dependencies163
Number of parent packages2
Max heaviness from parent packages157
Total heaviness from parent packages157
Number of parent packages (including Suggests and Enhances)2
Max co-heaviness from parent packages ("lumi" and "Biobase")6

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends utils methods graphics stats stats4 grDevices tools grid splines parallel BiocGenerics Biobase affy methylumi GenomicFeatures GenomicRanges annotate lattice mgcv nleqslv KernSmooth preprocessCore RSQLite DBI AnnotationDbi MASS affyio BiocManager zlibbioc scales reshape2 ggplot2 matrixStats FDb.InfiniumMethylation.hg19 minfi S4Vectors IRanges GenomeInfoDb SummarizedExperiment genefilter illuminaio RCurl XVector Biostrings BiocIO rtracklayer biomaRt XML xtable httr nlme Matrix bit64 blob memoise pkgconfig Rcpp plogr KEGGREST farver labeling lifecycle munsell R6 RColorBrewer rlang viridisLite plyr stringr digest glue 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 GenomeInfoDbData MatrixGenerics survival base64 bitops crayon Rsamtools GenomicAlignments restfulr progress BiocFileCache rappdirs xml2 curl jsonlite mime openssl bit vctrs cachem png 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 askpass cli fastmap utf8 rngtools clipr vroom cpp11 tzdb generics tidyselect purrr R.oo R.methodsS3 lambda.r futile.options assertthat sys formatR 0 0.5 1 Imported methods 0 50 100 150 Required packages 0 50 100 150 Heaviness from parents Biobase lumi In total 163 packages are required directly or indirectly (163) when installing 'lumiBarnes' (1.36.0) Depends Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'lumiBarnes' Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on lumiBarnes
lumi Depends Parent package is listed in Depends of lumiBarnes but no object from parent package is imported. 162 157
Biobase Depends Parent package is listed in Depends of lumiBarnes but no object from parent package is imported. 5 0

Analysis was done with pkgndep.