Dependency analysis on package oligoClasses
General information
| Bioconductor link | link |
|---|---|
| Package version | 1.58.0 |
| Number of strong dependencies | 48 |
| Number of all dependencies | 109 |
| Number of parent packages | 16 |
| Max heaviness from parent packages | 13 |
| Total heaviness from parent packages | 28 |
Number of parent packages (including Suggests and Enhances) | 35 |
| Max co-heaviness from parent packages ("RSQLite" and "DBI") | 1 |
Dependency heatmap
In the following dependency heatmap, rows are the parent packages of oligoClasses 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 oligoClasses.
Dependency table
"Import" information is from the NAMESPACE file of oligoClasses.
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 oligoClasses: number of required packages that can be reduced if moving parent package to Suggests of oligoClasses.
| Parent package | Field | imports | importMethods | importClasses | Required packages | Heaviness from parent on oligoClasses |
|---|---|---|---|---|---|---|
| RSQLite | Imports | Parent package is listed in Imports of oligoClasses but no object from parent package is imported. |
17 | 13 | ||
| SummarizedExperiment | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of oligoClasses. | 24 | 7 | ||
| foreach | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of oligoClasses. | 3 | 3 | ||
| Biostrings | Imports | 0 | 0 | 1 | 17 | 2 |
| BiocManager | Imports | 1 | 0 | 0 | 1 | 1 |
| affyio | Imports | 2 | 0 | 0 | 2 | 1 |
| ff | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of oligoClasses. | 2 | 1 | ||
| methods | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of oligoClasses. | 0 | 0 | ||
| graphics | Imports | 1 | 0 | 0 | 0 | 0 |
| utils | Imports | 4 | 0 | 0 | 0 | 0 |
| DBI | Imports | 0 | 2 | 0 | 1 | 0 |
| BiocGenerics | Imports | 4 | 0 | 0 | 4 | 0 |
| Biobase | Imports | 8 | 30 | 9 | 5 | 0 |
| S4Vectors | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of oligoClasses. | 6 | 0 | ||
| IRanges | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of oligoClasses. | 7 | 0 | ||
| GenomicRanges | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of oligoClasses. | 15 | 0 | ||
| VanillaICE | Suggests | No object is imported into the namespace of oligoClasses. | 83 | 36 | ||
| crlmm | Suggests | No object is imported into the namespace of oligoClasses. | 63 | 16 | ||
| pd.genomewidesnp.6 | Suggests | No object is imported into the namespace of oligoClasses. | 53 | 6 | ||
| pd.genomewidesnp.5 | Suggests | No object is imported into the namespace of oligoClasses. | 53 | 6 | ||
| pd.mapping50k.hind240 | Suggests | No object is imported into the namespace of oligoClasses. | 53 | 6 | ||
| pd.mapping50k.xba240 | Suggests | No object is imported into the namespace of oligoClasses. | 53 | 6 | ||
| pd.mapping250k.sty | Suggests | No object is imported into the namespace of oligoClasses. | 53 | 6 | ||
| pd.mapping250k.nsp | Suggests | No object is imported into the namespace of oligoClasses. | 53 | 6 | ||
| hapmapsnp5 | Suggests | No object is imported into the namespace of oligoClasses. | 0 | 1 | ||
| hapmapsnp6 | Suggests | No object is imported into the namespace of oligoClasses. | 0 | 1 | ||
| genomewidesnp6Crlmm | Suggests | No object is imported into the namespace of oligoClasses. | 1 | 1 | ||
| genomewidesnp5Crlmm | Suggests | No object is imported into the namespace of oligoClasses. | 1 | 1 | ||
| human370v1cCrlmm | Suggests | No object is imported into the namespace of oligoClasses. | 1 | 1 | ||
| RUnit | Suggests | No object is imported into the namespace of oligoClasses. | 3 | 1 | ||
| doRedis | Enhances | No object is imported into the namespace of oligoClasses. | 9 | 5 | ||
| doMPI | Enhances | No object is imported into the namespace of oligoClasses. | 7 | 4 | ||
| doMC | Enhances | No object is imported into the namespace of oligoClasses. | 5 | 2 | ||
| doSNOW | Enhances | No object is imported into the namespace of oligoClasses. | 5 | 2 | ||
| doParallel | Enhances | No object is imported into the namespace of oligoClasses. | 5 | 2 | ||
Analysis was done with pkgndep.