* using log directory ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/dnapath.Rcheck’
* using R version 4.3.0 beta (2023-04-07 r84200)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Big Sur 11.6.7
* using session charset: UTF-8
* checking for file ‘dnapath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dnapath’ version ‘0.7.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'GENIE3', 'reactome.db'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dnapath’ can be installed ... [11s/12s] OK
See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/dnapath-00install.html' for details.
* used C++ compiler: ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
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* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
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* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘GENIE3’
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* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
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* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] 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
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  Running ‘testthat.R’ [4s/4s]
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* checking running R code from vignettes ... [0s/0s] NONE
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* checking PDF version of manual ... [5s/5s] OK
* DONE
Status: 1 ERROR, 3 NOTEs
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 1:57