Dependency analysis on package xcms

General information

Bioconductor link link
Package version3.18.0
Number of strong dependencies93
Number of all dependencies144
Number of parent packages18
Max heaviness from parent packages43
Total heaviness from parent packages48
Number of parent packages (including Suggests and Enhances)38
Max co-heaviness from parent packages ("MsFeatures" and "SummarizedExperiment")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils stats graphics grDevices stats4 tools grid parallel splines BiocGenerics Rcpp glue S4Vectors MASS rlang R6 digest magrittr Biobase ProtGenerics IRanges clue cluster futile.logger snow codetools BH lambda.r futile.options formatR MsCoreUtils lattice lifecycle Matrix BiocParallel zlibbioc ellipsis pkgconfig vctrs cli crayon bitops scales ncdf4 Rhdf5lib BiocManager gtable tibble withr farver labeling munsell RColorBrewer viridisLite fansi pillar colorspace utf8 MatrixGenerics GenomicRanges GenomeInfoDb DelayedArray matrixStats XVector RCurl GenomeInfoDbData mzR plyr vsn affy impute pcaMethods MALDIquant mzID ggplot2 XML limma affyio preprocessCore doParallel foreach iterators isoband mgcv nlme DEoptimR SummarizedExperiment evaluate yaml xfun highr stringr stringi fs jsonlite knitr htmltools base64enc fastmap jquerylib tinytex bslib sass rappdirs survival hms prettyunits Spectra bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 xcms MSnbase RANN MassSpecWavelet robustbase MsFeatures graph htmlwidgets 0 20 40 Imported methods 0 20 40 60 80 Required packages 0 20 40 Heaviness from parents BiocParallel MSnbase methods RColorBrewer RANN MassSpecWavelet ProtGenerics plyr BiocGenerics Biobase lattice robustbase S4Vectors IRanges mzR MsCoreUtils SummarizedExperiment MsFeatures msdata ncdf4 magrittr caTools MALDIquant signal pander knitr multtest progress pheatmap Spectra rmarkdown MsBackendMgf BiocStyle testthat faahKO XML Rgraphviz rgl In total 93 packages are required directly or indirectly (144) when installing 'xcms' (3.18.0) Depends Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'xcms' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on xcms
MSnbase Depends 6 40 6 76 43
BiocParallel Depends The whole set of functions/methods/classes from parent package is imported to the namespace of xcms. 11 0
robustbase Imports 2 0 0 5 2
RANN Imports 1 0 0 0 1
MassSpecWavelet Imports 2 0 0 0 1
MsFeatures Imports 3 3 2 31 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of xcms. 0 0
RColorBrewer Imports The whole set of functions/methods/classes from parent package is imported to the namespace of xcms. 0 0
ProtGenerics Imports 0 10 1 1 0
plyr Imports 1 0 0 3 0
BiocGenerics Imports 5 0 0 4 0
Biobase Imports 1 6 1 5 0
lattice Imports 5 0 0 5 0
S4Vectors Imports 4 4 2 6 0
IRanges Imports 2 0 2 7 0
mzR Imports 4 0 0 10 0
MsCoreUtils Imports 3 0 0 12 0
SummarizedExperiment Imports 1 0 0 24 0
BiocStyle Suggests No object is imported into the namespace of xcms. 30 20
rmarkdown Suggests No object is imported into the namespace of xcms. 27 18
testthat Suggests No object is imported into the namespace of xcms. 36 15
knitr Suggests No object is imported into the namespace of xcms. 12 7
progress Suggests No object is imported into the namespace of xcms. 14 3
MsBackendMgf Suggests No object is imported into the namespace of xcms. 27 3
multtest Suggests No object is imported into the namespace of xcms. 14 2
Spectra Suggests No object is imported into the namespace of xcms. 26 2
faahKO Suggests No object is imported into the namespace of xcms. 94 2
msdata Suggests No object is imported into the namespace of xcms. 0 1
caTools Suggests No object is imported into the namespace of xcms. 1 1
signal Suggests No object is imported into the namespace of xcms. 6 1
pander Suggests No object is imported into the namespace of xcms. 8 1
pheatmap Suggests No object is imported into the namespace of xcms. 18 1
ncdf4 Suggests No object is imported into the namespace of xcms. 0 0
magrittr Suggests No object is imported into the namespace of xcms. 0 0
MALDIquant Suggests No object is imported into the namespace of xcms. 2 0
rgl Enhances No object is imported into the namespace of xcms. 23 13
Rgraphviz Enhances No object is imported into the namespace of xcms. 9 2
XML Enhances No object is imported into the namespace of xcms. 2 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 xcms Co-heaviness as Jaccard coeffcient
SummarizedExperiment MsFeatures 11 0.917

Analysis was done with pkgndep.