* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/MACP.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 ‘MACP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MACP’ version ‘0.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘orthogene’
* 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 ‘MACP’ can be installed ... [48s/60s] 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [14s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/16s] OK
* checking whether the package can be unloaded cleanly ... [14s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/17s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/19s] OK
* checking loading without being on the library search path ... [14s/17s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘fmsb’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [68s/96s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘orthogene’ in Rd xrefs
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/31s] ERROR
Running examples in ‘MACP-Ex.R’ failed
The error most likely occurred in:

> ### Name: MCL_clustering
> ### Title: MCL clustering
> ### Aliases: MCL_clustering
> 
> ### ** Examples
> 
> # open high-confidence network
> hc_ppi <-
+ read.delim(
+ system.file("extdata/ppi_input_ClusterONE.txt", package = "MACP"),
+ header = FALSE)
> # predict complexes by ClusterONE
> predcpx <-
+ get_clusters(csize = 3, d = 0.3, p = 2,
+ max_overlap = 0.8,
+ tpath = file.path(system.file("extdata", package = "MACP")))
> # Break down big complexes by MCL
> MCL_clusters <- MCL_clustering(hc_ppi, predcpx, inflation = 4, csize = 2)
Error in loadNamespace(x) : there is no package called ‘MCL’
Calls: MCL_clustering ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MACP_tutorial.Rmd’ using rmarkdown
Error: processing vignette 'MACP_tutorial.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘MACP_tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘MACP_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [8s/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: 2 ERRORs, 3 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/MACP.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 9:21.00, 376.62 + 38.44