Dependency analysis on package CytoML

General information

Bioconductor link link
Package version2.8.0
Number of strong dependencies125
Number of all dependencies154
Number of parent packages32
Max heaviness from parent packages37
Total heaviness from parent packages41
Number of parent packages (including Suggests and Enhances)37
Max co-heaviness from parent packages ("openCyto" and "corpcor")1

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests methods utils stats graphics grDevices stats4 tools grid splines parallel tcltk BiocGenerics glue magrittr Rcpp rlang BH lifecycle vctrs pillar ellipsis fansi pkgconfig cli crayon utf8 R6 graph RcppParallel RProtoBufLib Rhdf5lib RcppArmadillo tibble digest jsonlite Biobase matrixStats cytolib S4Vectors generics tidyselect purrr withr base64enc lattice latticeExtra XML ggplot2 RBGL Rgraphviz data.table dplyr scales aws.s3 aws.signature flowCore ncdfFlow DelayedArray png jpeg RColorBrewer gtable isoband MASS mgcv farver labeling munsell viridisLite curl httr xml2 zlibbioc Matrix MatrixGenerics IRanges nlme colorspace mime openssl askpass sys flowWorkspace plyr hexbin gridExtra gtools flowViz flowStats flowClust clue ks rrcov R.utils KernSmooth IDPmisc fda cluster corpcor mnormt FNN kernlab mclust multicool mvtnorm plot3D pracma robustbase pcaPP R.oo R.methodsS3 fds deSolve misc3d DEoptimR rainbow RCurl hdrcde bitops locfit ash evaluate highr stringr yaml xfun stringi bslib htmltools jquerylib knitr tinytex sass fastmap fs rappdirs brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 0 20 40 Imported methods 0 50 100 Required packages 0 10 20 30 Heaviness from parents methods graphics utils base64enc grDevices yaml stats RcppParallel data.table jsonlite corpcor xml2 XML plyr RUnit Biobase lattice graph RBGL cytolib Rgraphviz tibble flowCore dplyr flowWorkspace ggcyto openCyto BH RProtoBufLib Rhdf5lib Rcpp RcppArmadillo flowWorkspaceData parallel knitr rmarkdown testthat In total 125 packages are required directly or indirectly (154) when installing 'CytoML' (2.8.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'CytoML' Imported functions 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 CytoML.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on CytoML
openCyto Imports Parent package is listed in Imports of CytoML but no object from parent package is imported. 120 37
ggcyto Imports 1 0 0 84 2
yaml Imports 1 0 0 0 1
RUnit Imports Parent package is listed in Imports of CytoML but no object from parent package is imported. 3 1
methods Imports 7 0 10 0 0
graphics Imports 3 0 0 0 0
utils Imports 3 0 0 0 0
base64enc Imports 2 0 0 0 0
grDevices Imports 1 0 0 0 0
stats Imports Parent package is listed in Imports of CytoML but no object from parent package is imported. 0 0
RcppParallel Imports 1 0 0 0 0
data.table Imports The whole set of functions/methods/classes from parent package is imported to the namespace of CytoML. 1 0
jsonlite Imports 2 0 0 1 0
corpcor Imports Parent package is listed in Imports of CytoML but no object from parent package is imported. 1 0
xml2 Imports 4 0 0 1 0
XML Imports 20 0 0 2 0
plyr Imports 2 0 0 3 0
Biobase Imports 0 0 1 5 0
lattice Imports Parent package is listed in Imports of CytoML but no object from parent package is imported. 5 0
graph Imports 11 0 3 6 0
RBGL Imports 1 0 0 8 0
cytolib Imports 1 0 0 9 0
Rgraphviz Imports 2 0 0 9 0
tibble Imports 1 0 0 15 0
flowCore Imports 23 0 0 17 0
dplyr Imports 8 0 0 20 0
flowWorkspace Imports 55 0 0 80 0
BH LinkingTo Parent package is listed in LinkingTo of CytoML but no object from parent package is imported. 0 0
RProtoBufLib LinkingTo Parent package is listed in LinkingTo of CytoML but no object from parent package is imported. 0 0
Rhdf5lib LinkingTo Parent package is listed in LinkingTo of CytoML but no object from parent package is imported. 0 0
Rcpp LinkingTo Parent package is listed in LinkingTo of CytoML but no object from parent package is imported. 2 0
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of CytoML but no object from parent package is imported. 4 0
rmarkdown Suggests No object is imported into the namespace of CytoML. 27 15
testthat Suggests No object is imported into the namespace of CytoML. 36 14
knitr Suggests No object is imported into the namespace of CytoML. 12 6
flowWorkspaceData Suggests No object is imported into the namespace of CytoML. 0 1
parallel Suggests No object is imported into the namespace of CytoML. 0 0

Analysis was done with pkgndep.