Dependency analysis on package graphite

General information

Bioconductor link link
Package version1.42.0
Number of strong dependencies47
Number of all dependencies184
Number of parent packages9
Max heaviness from parent packages29
Total heaviness from parent packages31
Number of parent packages (including Suggests and Enhances)27
Max co-heaviness from parent packages ("AnnotationDbi" and "httr")9

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats tools graphics grDevices stats4 grid parallel splines BiocGenerics jsonlite R6 glue rlang fastmap curl mime openssl askpass sys Biobase vctrs crayon cli RCurl bitops pkgconfig httr IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise Rcpp plogr png Biostrings bit cachem XVector GenomeInfoDb zlibbioc GenomeInfoDbData digest magrittr yaml evaluate stringr stringi AnnotationDbi graph XML rappdirs ellipsis lifecycle pillar fansi utf8 xfun highr Rgraphviz htmltools base64enc fs BiocManager tibble withr backports KEGGgraph knitr jquerylib tinytex bslib sass org.Hs.eg.db RColorBrewer Matrix igraph gRbase qpgraph RBGL lattice RcppEigen RcppArmadillo annotate BiocParallel GenomicRanges GenomicFeatures mvtnorm qtl BH xtable futile.logger snow codetools BiocIO rtracklayer biomaRt lambda.r futile.options Rsamtools GenomicAlignments restfulr progress BiocFileCache xml2 formatR Rhtslib SummarizedExperiment rjson hms prettyunits dbplyr dplyr filelock MatrixGenerics DelayedArray assertthat purrr tidyselect generics matrixStats R.methodsS3 R.oo R.utils R.cache bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 RJSONIO uuid uchardet base64url IRkernel IRdisplay repr pbdZMQ corpcor fields spam viridis maps dotCall64 viridisLite ggplot2 gridExtra gtable isoband MASS mgcv scales nlme farver labeling munsell colorspace 0 2 4 6 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents methods rappdirs stats utils graphics rlang graph httr AnnotationDbi codetools impute parallel checkmate a4Preproc ALL R.rsp knitr SPIA rmarkdown BiocStyle testthat org.Hs.eg.db hgu133plus2.db hgu95av2.db RCy3 clipper topologyGSA In total 47 packages are required directly or indirectly (184) when installing 'graphite' (1.42.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'graphite' Imported functions Imported S4 methods Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on graphite
methods Depends 2 0 0 0 0
AnnotationDbi Imports 2 0 0 44 29
rappdirs Imports 1 0 0 0 1
graph Imports 0 7 0 6 1
stats Imports 1 0 0 0 0
utils Imports 3 0 0 0 0
graphics Imports 1 0 0 0 0
rlang Imports Parent package is listed in Imports of graphite but no object from parent package is imported. 1 0
httr Imports 3 0 0 9 0
topologyGSA Suggests No object is imported into the namespace of graphite. 130 84
clipper Suggests No object is imported into the namespace of graphite. 112 66
testthat Suggests No object is imported into the namespace of graphite. 36 23
RCy3 Suggests No object is imported into the namespace of graphite. 46 22
BiocStyle Suggests No object is imported into the namespace of graphite. 30 20
rmarkdown Suggests No object is imported into the namespace of graphite. 27 17
knitr Suggests No object is imported into the namespace of graphite. 12 8
R.rsp Suggests No object is imported into the namespace of graphite. 9 6
SPIA Suggests No object is imported into the namespace of graphite. 14 5
checkmate Suggests No object is imported into the namespace of graphite. 2 2
hgu133plus2.db Suggests No object is imported into the namespace of graphite. 46 2
hgu95av2.db Suggests No object is imported into the namespace of graphite. 46 2
codetools Suggests No object is imported into the namespace of graphite. 0 1
impute Suggests No object is imported into the namespace of graphite. 0 1
parallel Suggests No object is imported into the namespace of graphite. 0 1
a4Preproc Suggests No object is imported into the namespace of graphite. 6 1
ALL Suggests No object is imported into the namespace of graphite. 6 1
org.Hs.eg.db Suggests No object is imported into the namespace of graphite. 45 1

Analysis was done with pkgndep.