Last updated on 2025-02-22 06:51:29 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-fedora-clang | 0.7.6 | 281.47 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.7.6 | 223.62 | OK | |||
| r-devel-macos-x86_64 | 0.7.6 | 224.00 | OK | |||
| r-release-macos-arm64 | 0.7.4 | 121.00 | NOTE | |||
| r-release-macos-x86_64 | 0.7.6 | 228.00 | OK | |||
| r-oldrel-macos-arm64 | 0.7.4 | 117.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.7.6 | 209.00 | NOTE |
Version: 0.7.4
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘reactome.db’
Flavor: r-release-macos-arm64
Version: 0.7.4
Check: C++ specification
Result: NOTE
Specified C++11: please drop specification unless essential
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64
Version: 0.7.4
Check: Rd metadata
Result: NOTE
Invalid package aliases in Rd file 'dnapath2-package.Rd':
‘dnapath2-package’
Flavor: r-release-macos-arm64
Version: 0.7.4
Check: Rd contents
Result: NOTE
Auto-generated content requiring editing in Rd file 'dnapath2-package.Rd':
\references: ‘This optional section can contain literature or other refere...’
\seealso: ‘Optional links to other man pages’
\examples: ‘\dontrun{ ## Optional simple examples of the most impor...’
Flavor: r-release-macos-arm64
Version: 0.7.4
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking: 'GENIE3', 'reactome.db'
Flavor: r-oldrel-macos-arm64
Version: 0.7.4
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘GENIE3’
Flavor: r-oldrel-macos-arm64
Version: 0.7.4
Check: examples
Result: ERROR
Running examples in ‘dnapath-Ex.R’ failed
The error most likely occurred in:
> ### Name: run_genie3
> ### Title: Wrapper for GENIE3 method
> ### Aliases: run_genie3
>
> ### ** Examples
>
> if(!requireNamespace("GENIE3", quietly = TRUE)) {
+ data(meso)
+ data(p53_pathways)
+
+ # To create a short example, we subset on two pathways from the p53 pathway list,
+ # and will only run 5 permutations for significance testing.
+ pathway_list <- p53_pathways[c(8, 13)]
+ n_perm <- 5
+
+ # Use this method to perform differential network analysis.
+ # The parameters in run_genie3() can be adjusted using the ... argument.
+ # For example, the 'nTrees' parameter can be specified as shown here.
+ results <- dnapath(x = meso$gene_expression,
+ pathway_list = pathway_list,
+ group_labels = meso$groups,
+ n_perm = n_perm,
+ network_inference = run_genie3,
+ nTrees = 100)
+ summary(results)
+
+ # The group-specific association matrices can be extracted using get_networks().
+ nw_list <- get_networks(results[[1]]) # Get networks for pathway 1.
+
+ # nw_list has length 2 and contains the inferred networks for the two groups.
+ # The gene names are the Entrezgene IDs from the original expression dataset.
+ # Renaming the genes in the dnapath results to rename those in the networks.
+ # NOTE: The temporary directory, tempdir(), is used in this example. In practice,
+ # this argument can be removed or changed to an existing directory
+ results <- rename_genes(results, to = "symbol", species = "human",
+ dir_save = tempdir())
+ nw_list <- get_networks(results[[1]]) # The genes (columns) will have new names.
+
+ # (Optional) Plot the network using SeqNet package (based on igraph plotting).
+ # First rename entrezgene IDs into gene symbols.
+ SeqNet::plot_network(nw_list[[1]])
+ }
Warning: The `GENIE3` package must be installed to use run_genie3(). Using run_corr() instead.
Error in wCorr::weightedCorr(x[, index_set[1, i]], x[, index_set[2, i]], :
The vectors ‘x’, ‘y’, and ‘weights’ must all be of the same length.
Calls: dnapath ... network_inference -> run_corr -> sapply -> lapply -> FUN -> <Anonymous>
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.7.6
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘reactome.db’
Flavor: r-oldrel-macos-x86_64