* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/dnapath.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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
Package suggested but not available for checking: ‘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 ... [60s/76s] OK
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [24s/29s] OK
* checking Rd files ... OK
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'dnapath2-package.Rd':
  ‘dnapath2-package’
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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...’
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [45s/65s] ERROR
Running examples in ‘dnapath-Ex.R’ failed
The error most likely occurred in:

> ### Name: run_dwlasso
> ### Title: Wrapper for degree-weighted lasso method
> ### Aliases: run_dwlasso
> 
> ### ** Examples
> 
> data(meso)
> data(p53_pathways)
> 
> # To create a short example, we subset on two pathways from the p53 pathway list,
> # and will only run 1 permutation for significance testing.
> pathway_list <- p53_pathways[c(8, 13)]
> n_perm <- 1
> 
> # Use this method to perform differential network analysis.
> # The parameters in run_dwlasso() can be adjusted using the ... argument.
> # For example, the 'lambda1' 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_dwlasso,
+                    lambda1 = 0.5)
Warning: The `DWLasso` package must be installed to use run_dwlasso(). 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 ...
  Running ‘testthat.R’ [20s/25s]
 [21s/25s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [11s/14s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/dnapath.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:19.05, 227.59 + 18.86