Check results for 'dnapath'

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 the install log 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
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [2s/3s] OK
checking Rd files ... [1s/1s] OK
checking Rd metadata ... OK
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘GENIE3’
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking compilation flags in Makevars ... OK
checking for GNU extensions in Makefiles ... OK
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking use of PKG_*FLAGS in Makefiles ... OK
checking compiled code ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [9s/9s] ERROR Running examples in ‘dnapath-Ex.R’ failed The error most likely occurred in: > ### Name: run_genie3 > ### Title: Wrapper for GENIE3 method > ### Aliases: run_genie3 > > ### ** Examples > > if(!requireNamespace("GENIE3", quietly = TRUE)) { + data(meso) + data(p53_pathways) + + # To create a short example, we subset on two pathways from the p53 pathway list, + # and will only run 5 permutations for significance testing. + pathway_list <- p53_pathways[c(8, 13)] + n_perm <- 5 + + # Use this method to perform differential network analysis. + # The parameters in run_genie3() can be adjusted using the ... argument. + # For example, the 'nTrees' parameter can be specified as shown here. + results <- dnapath(x = meso$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
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [4s/4s] OK Running ‘testthat.R’ [4s/4s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [0s/0s] NONE ‘introduction_to_dnapath.Rmd’ using ‘UTF-8’... [0s/0s] OK ‘package_data.Rmd’ using ‘UTF-8’... [0s/0s] OK
checking re-building of vignette outputs ... [25s/55s] OK
checking PDF version of manual ... [5s/5s] OK
DONE Status: 1 ERROR, 3 NOTEs
using check arguments '--no-clean-on-error '