[ Started: 2026-02-13 04:33:57 CET ]
[ cosmosR v1.16.0 for BioC-3.21 from https://git.bioconductor.org/packages/cosmosR@RELEASE_3_21 (c5fbdd3 2025-04-15 12:30:23) ]

* using log directory ‘/mnt/disk0/build/bioc-check/cosmosr/bioc-3.21/2026-02-13_0429/cosmosR/cosmosR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘cosmosR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cosmosR’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘cosmosR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.4Mb
    help   1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘keep_controllable_neighbours’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
decompress_solution_network: no visible binding for global variable
  ‘HMDB_mapper_vec’
format_COSMOS_res: no visible binding for global variable
  ‘HMDB_mapper_vec’
meta_network_cleanup: no visible binding for global variable ‘target’
meta_network_cleanup: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . HMDB_mapper_vec target
* checking Rd files ... OK
* checking Rd metadata ... 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 ... 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cosmosR-Ex.R’ failed
The error most likely occurred in:

> ### Name: meta_network_cleanup
> ### Title: meta_network_cleanup
> ### Aliases: meta_network_cleanup
> 
> ### ** Examples
> 
> # Create a meta network data frame
> example_meta_network <- data.frame(
+ source = c("A", "B", "C", "D", "A", "B", "C", "D", "A"),
+ interaction = c(1, 1, 1, -1, 1, -1, 1, -1, 1),
+ target = c("B", "C", "D", "A", "C", "D", "A", "B", "B")
+ )
> 
> # Clean up the example meta network
> cleaned_meta_network <- meta_network_cleanup(example_meta_network)
Error:
! `summarise_each()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `across()` instead.
Backtrace:
    ▆
 1. ├─cosmosR::meta_network_cleanup(example_meta_network)
 2. │ └─meta_network %>% group_by(source, target) %>% ...
 3. └─dplyr::summarise_each(., funs(mean(., na.rm = TRUE)))
 4.   └─dplyr:::each_defunct("summarise_each()")
 5.     └─lifecycle::deprecate_stop(when = "0.7.0", what = fun, with = "across()")
 6.       └─lifecycle:::deprecate_stop0(msg)
 7.         └─rlang::cnd_signal(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/cosmosr/bioc-3.21/2026-02-13_0429/cosmosR/cosmosR.Rcheck/00check.log’
for details.

[ Finished: 2026-02-13 04:34:55 CET ]