Dependency analysis on package MSnbase

General information

Bioconductor link link
Package version2.22.0
Number of strong dependencies76
Number of all dependencies254
Number of parent packages25
Max heaviness from parent packages7
Total heaviness from parent packages23
Number of parent packages (including Suggests and Enhances)48
Max co-heaviness from parent packages ("vsn" and "ggplot2")18

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics grDevices grid stats4 parallel splines tools datasets glue rlang BiocGenerics R6 magrittr Rcpp digest crayon Biobase lifecycle withr ellipsis cli pkgconfig vctrs MASS lattice tibble fansi pillar utf8 S4Vectors BiocManager zlibbioc Matrix codetools farver labeling munsell RColorBrewer viridisLite colorspace gtable ProtGenerics affyio preprocessCore isoband mgcv scales nlme ncdf4 Rhdf5lib futile.logger snow BH lambda.r futile.options formatR XML plyr doParallel foreach iterators clue cluster affy limma ggplot2 jsonlite evaluate stringr stringi yaml fastmap highr xfun htmltools base64enc rappdirs bitops knitr mime bslib sass jquerylib fs IRanges RCurl httr curl openssl askpass sys commonmark purrr cachem impute pcaMethods htmlwidgets XVector GenomeInfoDb GenomeInfoDbData xml2 xtable httpuv fontawesome sourcetools later promises BiocFileCache DBI assertthat dplyr generics tidyselect RSQLite dbplyr filelock bit64 blob memoise plogr bit gtools KernSmooth mvtnorm progress hms prettyunits tinytex desc pkgload rprojroot rstudioapi cpp11 MSnbase BiocParallel mzR MsCoreUtils vsn MALDIquant mzID shiny AnnotationDbi crosstalk KEGGREST lazyeval png Biostrings caTools lobstr tmvtnorm norm gmm sandwich zoo MatrixGenerics GenomicRanges DelayedArray matrixStats brew bookdown rmarkdown brio callr praise processx ps waldo diffobj rematch2 BiocVersion interactiveDisplayBase DT MLInterfaces mclust caret e1071 sampling class kernlab nnet randomForest proxy FNN hexbin dendextend LaplacesDemon coda mixtools biomaRt RcppArmadillo annotate gdata pls sfsmisc rpart genefilter fpc ggvis gbm hwriter threejs mlbench ModelMetrics pROC recipes reshape2 lpSolve viridis segmented survival flexmix prabclus diptest robustbase igraph data.table gower hardhat ipred lubridate tidyr timeDate gridExtra modeltools DEoptimR prodlim lava future.apply progressr numDeriv SQUAREM future globals listenv parallelly 0 10 20 30 Imported methods 0 100 200 Required packages 0 50 100 Heaviness from parents methods ProtGenerics BiocGenerics Biobase S4Vectors mzR grid stats4 impute digest MALDIquant XML Rcpp plyr lattice MASS IRanges pcaMethods BiocParallel affy mzID MsCoreUtils scales ggplot2 vsn msdata magrittr norm microbenchmark Rdisop gridExtra zoo gplots knitr pryr imputeLCMD rgl SummarizedExperiment rols rmarkdown roxygen2 BiocStyle shiny testthat rpx pRolocdata AnnotationHub pRoloc In total 76 packages are required directly or indirectly (254) when installing 'MSnbase' (2.22.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'MSnbase' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on MSnbase
mzR Depends The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 10 3
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 0 0
ProtGenerics Depends 0 1 1 1 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 4 0
Biobase Depends The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 5 0
S4Vectors Depends 6 5 1 6 0
BiocParallel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 11 7
mzID Imports 2 0 2 11 4
MsCoreUtils Imports 7 0 0 12 3
vsn Imports 1 0 0 46 2
impute Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 0 1
MALDIquant Imports 2 0 0 2 1
IRanges Imports 8 0 1 7 1
pcaMethods Imports 2 0 0 9 1
grid Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 0 0
stats4 Imports 1 0 0 0 0
digest Imports 1 0 0 1 0
XML Imports 4 0 0 2 0
Rcpp Imports 1 0 0 2 0
plyr Imports 3 0 0 3 0
lattice Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 5 0
MASS Imports 1 0 0 5 0
affy Imports 3 0 0 11 0
scales Imports The whole set of functions/methods/classes from parent package is imported to the namespace of MSnbase. 15 0
ggplot2 Imports 29 0 0 37 0
pRoloc Suggests No object is imported into the namespace of MSnbase. 208 133
AnnotationHub Suggests No object is imported into the namespace of MSnbase. 85 57
rpx Suggests No object is imported into the namespace of MSnbase. 50 30
BiocStyle Suggests No object is imported into the namespace of MSnbase. 30 21
shiny Suggests No object is imported into the namespace of MSnbase. 34 20
rmarkdown Suggests No object is imported into the namespace of MSnbase. 27 19
roxygen2 Suggests No object is imported into the namespace of MSnbase. 30 18
testthat Suggests No object is imported into the namespace of MSnbase. 36 16
rgl Suggests No object is imported into the namespace of MSnbase. 23 14
rols Suggests No object is imported into the namespace of MSnbase. 27 12
SummarizedExperiment Suggests No object is imported into the namespace of MSnbase. 24 11
knitr Suggests No object is imported into the namespace of MSnbase. 12 8
imputeLCMD Suggests No object is imported into the namespace of MSnbase. 21 7
gplots Suggests No object is imported into the namespace of MSnbase. 7 5
pryr Suggests No object is imported into the namespace of MSnbase. 14 5
pRolocdata Suggests No object is imported into the namespace of MSnbase. 77 2
msdata Suggests No object is imported into the namespace of MSnbase. 0 1
norm Suggests No object is imported into the namespace of MSnbase. 1 1
microbenchmark Suggests No object is imported into the namespace of MSnbase. 2 1
Rdisop Suggests No object is imported into the namespace of MSnbase. 3 1
gridExtra Suggests No object is imported into the namespace of MSnbase. 5 1
zoo Suggests No object is imported into the namespace of MSnbase. 6 1
magrittr Suggests No object is imported into the namespace of MSnbase. 0 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 MSnbase Co-heaviness as Jaccard coeffcient
ggplot2 vsn 18 0.9

Analysis was done with pkgndep.