Dependency analysis on package pRoloc

General information

Bioconductor link link
Package version1.36.0
Number of strong dependencies208
Number of all dependencies243
Number of parent packages38
Max heaviness from parent packages36
Total heaviness from parent packages105
Number of parent packages (including Suggests and Enhances)56
Max co-heaviness from parent packages ("biomaRt" and "MLInterfaces")27

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports LinkingTo Suggests utils stats methods grDevices graphics grid tools splines stats4 parallel datasets glue rlang R6 magrittr digest cli crayon lattice MASS Rcpp pkgconfig vctrs lifecycle tibble withr ellipsis fansi pillar utf8 Matrix RColorBrewer nlme jsonlite BiocGenerics mgcv farver labeling munsell viridisLite colorspace fastmap stringr stringi Biobase S4Vectors IRanges scales zlibbioc gtable isoband yaml evaluate ggplot2 curl purrr highr xfun codetools plyr XML cluster DBI httr htmltools mime cachem base64enc RSQLite KEGGREST openssl generics tidyselect bit64 blob memoise plogr png Biostrings askpass rappdirs bit XVector GenomeInfoDb sys RCurl GenomeInfoDbData bitops futile.logger snow BH lambda.r futile.options formatR BiocManager foreach iterators AnnotationDbi survival class dplyr bslib sass jquerylib fs mzR ProtGenerics MsCoreUtils BiocParallel vsn affy impute pcaMethods MALDIquant mzID ncdf4 Rhdf5lib clue limma affyio preprocessCore doParallel rpart kernlab assertthat commonmark htmlwidgets nnet proxy viridis gridExtra xml2 cpp11 annotate gdata pls sfsmisc genefilter fpc ggvis shiny gbm hwriter threejs mlbench xtable gtools mclust flexmix prabclus diptest robustbase httpuv fontawesome sourcetools later promises igraph crosstalk modeltools DEoptimR lazyeval lpSolve segmented progress BiocFileCache hms prettyunits dbplyr filelock e1071 ModelMetrics pROC recipes reshape2 data.table gower hardhat ipred lubridate tidyr timeDate prodlim KernSmooth lava future.apply progressr numDeriv SQUAREM future globals listenv parallelly knitr tinytex desc pkgload rprojroot rstudioapi sp permute brew bookdown rmarkdown brio callr praise processx ps waldo diffobj rematch2 spam maps dotCall64 MSnbase 0 10 20 Imported methods 0 50 100 Required packages 0 10 20 30 Heaviness from parents methods Rcpp BiocParallel MSnbase MLInterfaces stats4 FNN stats RColorBrewer utils grDevices graphics randomForest nnet proxy mvtnorm gtools plyr mclust kernlab BiocGenerics Biobase lattice MASS LaplacesDemon class coda sampling hexbin e1071 knitr mixtools scales ggplot2 dendextend biomaRt caret RcppArmadillo nipals hpar xtable Rtsne reshape magick akima vegan dplyr rgl rmarkdown roxygen2 BiocStyle testthat fields AnnotationDbi GO.db pRolocdata In total 208 packages are required directly or indirectly (243) when installing 'pRoloc' (1.36.0) Depends Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'pRoloc' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on pRoloc
MLInterfaces Depends 7 4 0 112 36
MSnbase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 76 18
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 0 0
Rcpp Depends The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 2 0
BiocParallel Depends 2 0 0 11 0
caret Imports 3 0 0 81 24
biomaRt Imports 3 0 1 70 8
knitr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 12 4
dendextend Imports 1 0 0 41 4
sampling Imports 1 0 0 7 2
mixtools Imports 1 0 0 14 2
FNN Imports 2 0 0 0 1
randomForest Imports 1 0 0 1 1
mvtnorm Imports 2 0 0 2 1
LaplacesDemon Imports 2 0 0 5 1
coda Imports 3 0 0 6 1
hexbin Imports 1 0 0 7 1
stats4 Imports 1 0 0 0 0
stats Imports 20 0 0 0 0
RColorBrewer Imports 1 0 0 0 0
utils Imports 8 0 0 0 0
grDevices Imports 5 0 0 0 0
graphics Imports 15 0 0 0 0
nnet Imports 1 0 0 2 0
proxy Imports 1 0 0 2 0
gtools Imports 1 0 0 3 0
plyr Imports 3 0 0 3 0
mclust Imports 3 0 0 4 0
kernlab Imports 6 0 0 4 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 4 0
Biobase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 5 0
lattice Imports The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 5 0
MASS Imports The whole set of functions/methods/classes from parent package is imported to the namespace of pRoloc. 5 0
class Imports 1 0 0 6 0
e1071 Imports 3 0 0 8 0
scales Imports 1 0 0 15 0
ggplot2 Imports 28 0 0 37 0
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of pRoloc but no object from parent package is imported. 4 1
testthat Suggests No object is imported into the namespace of pRoloc. 36 13
roxygen2 Suggests No object is imported into the namespace of pRoloc. 30 6
BiocStyle Suggests No object is imported into the namespace of pRoloc. 30 4
fields Suggests No object is imported into the namespace of pRoloc. 43 4
akima Suggests No object is imported into the namespace of pRoloc. 8 2
vegan Suggests No object is imported into the namespace of pRoloc. 14 2
rmarkdown Suggests No object is imported into the namespace of pRoloc. 27 2
nipals Suggests No object is imported into the namespace of pRoloc. 0 1
hpar Suggests No object is imported into the namespace of pRoloc. 1 1
Rtsne Suggests No object is imported into the namespace of pRoloc. 4 1
reshape Suggests No object is imported into the namespace of pRoloc. 4 1
magick Suggests No object is imported into the namespace of pRoloc. 5 1
rgl Suggests No object is imported into the namespace of pRoloc. 23 1
GO.db Suggests No object is imported into the namespace of pRoloc. 45 1
pRolocdata Suggests No object is imported into the namespace of pRoloc. 77 1
xtable Suggests No object is imported into the namespace of pRoloc. 2 0
dplyr Suggests No object is imported into the namespace of pRoloc. 20 0
AnnotationDbi Suggests No object is imported into the namespace of pRoloc. 44 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 pRoloc Co-heaviness as Jaccard coeffcient
MLInterfaces biomaRt 27 0.38

Analysis was done with pkgndep.