Dependency analysis on package metagenomeSeq

General information

Bioconductor link link
Package version1.38.0
Number of strong dependencies30
Number of all dependencies151
Number of parent packages15
Max heaviness from parent packages6
Total heaviness from parent packages17
Number of parent packages (including Suggests and Enhances)24
Max co-heaviness from parent packages ("foreach" and "glmnet")3

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils stats methods graphics grDevices grid splines tools stats4 lattice BiocGenerics Matrix Rcpp bitops survival codetools iterators foreach shape RcppEigen gtools caTools KernSmooth limma matrixStats locfit glue jsonlite magrittr R6 pkgconfig rlang vctrs crayon cli evaluate stringr yaml stringi plyr MASS mgcv nlme digest ellipsis lifecycle withr fansi tibble pillar utf8 AnnotationDbi XML Biobase DBI xtable httr IRanges RSQLite S4Vectors KEGGREST curl mime openssl bit64 blob memoise plogr png Biostrings askpass bit cachem XVector GenomeInfoDb sys fastmap zlibbioc RCurl GenomeInfoDbData slam lpsymphony fdrtool highr xfun rhdf5 Rhdf5lib rhdf5filters permute cluster brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 interactiveDisplayBase shiny RColorBrewer ggplot2 reshape2 gridSVG Category DT httpuv fontawesome htmltools sourcetools later promises commonmark bslib gtable isoband scales graph RBGL GSEABase genefilter annotate htmlwidgets crosstalk jquerylib base64enc sass farver labeling munsell viridisLite BH lazyeval fs rappdirs colorspace 0 10 20 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents methods RColorBrewer Biobase limma glmnet parallel matrixStats graphics grDevices stats utils foreach Matrix gplots Wrench gss BiocGenerics IHW knitr biomformat vegan testthat annotate interactiveDisplay In total 30 packages are required directly or indirectly (151) when installing 'metagenomeSeq' (1.38.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'metagenomeSeq' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on metagenomeSeq
glmnet Depends The whole set of functions/methods/classes from parent package is imported to the namespace of metagenomeSeq. 16 6
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of metagenomeSeq. 5 2
RColorBrewer Depends The whole set of functions/methods/classes from parent package is imported to the namespace of metagenomeSeq. 0 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of metagenomeSeq. 0 0
limma Depends The whole set of functions/methods/classes from parent package is imported to the namespace of metagenomeSeq. 5 0
gplots Imports 1 0 0 7 5
Wrench Imports The whole set of functions/methods/classes from parent package is imported to the namespace of metagenomeSeq. 10 2
parallel Imports 4 0 0 0 1
matrixStats Imports 2 0 0 0 0
graphics Imports 6 0 0 0 0
grDevices Imports 2 0 0 0 0
stats Imports 26 0 0 0 0
utils Imports 4 0 0 0 0
foreach Imports 2 0 0 3 0
Matrix Imports 1 0 0 7 0
interactiveDisplay Suggests No object is imported into the namespace of metagenomeSeq. 106 92
annotate Suggests No object is imported into the namespace of metagenomeSeq. 47 39
testthat Suggests No object is imported into the namespace of metagenomeSeq. 36 32
knitr Suggests No object is imported into the namespace of metagenomeSeq. 12 10
biomformat Suggests No object is imported into the namespace of metagenomeSeq. 14 6
vegan Suggests No object is imported into the namespace of metagenomeSeq. 14 6
IHW Suggests No object is imported into the namespace of metagenomeSeq. 9 4
gss Suggests No object is imported into the namespace of metagenomeSeq. 1 1
BiocGenerics Suggests No object is imported into the namespace of metagenomeSeq. 4 0

Analysis was done with pkgndep.