[ Started: 2024-03-30 13:18:34 CET ]
[ decoupleR v2.9.7 for BioC-3.18 from https://github.com/saezlab/decoupleR@master (32a65ca 2024-03-28 16:32:58) ]

* using log directory ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.18/2024-03-30_1314/decoupleR/decoupleR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.9.7’
* 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 ‘decoupleR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc       6.6Mb
    extdata   1.5Mb
* 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 ... 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
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 13:19:00] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Contains 6 files.
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 13:19:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 13:19:00] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'run_gsva.Rd':
  ‘GSVA::gsva’ ‘GeneSetCollection’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:

> ### Name: run_gsva
> ### Title: Gene Set Variation Analysis (GSVA)
> ### Aliases: run_gsva
> 
> ### ** Examples
> 
> inputs_dir <- system.file("testdata", "inputs", package = "decoupleR")
> 
> mat <- readRDS(file.path(inputs_dir, "mat.rds"))
> net <- readRDS(file.path(inputs_dir, "net.rds"))
> 
> run_gsva(mat, net, minsize=1, verbose = FALSE)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘gsva’ for signature ‘"missing", "missing"’
Calls: run_gsva ... rownames_to_column -> as.data.frame -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      <environment>)`: unable to find an inherited method for function 'gsva' for signature '"missing", "missing"'
  Backtrace:
      ▆
   1. ├─decoupleR::run_gsva(mat, net, minsize = 1L, verbose = FALSE) at test-statistic-gsva.R:22:5
   2. │ └─... %>% ...
   3. ├─dplyr::mutate(...)
   4. ├─tidyr::pivot_longer(...)
   5. ├─tibble::rownames_to_column(., var = "source")
   6. ├─base::as.data.frame(.)
   7. └─GSVA::gsva(param = ., verbose = verbose)
   8.   └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 33 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘decoupleR.Rmd’ using ‘UTF-8’... OK
  ‘pw_bk.Rmd’ using ‘UTF-8’... OK
  ‘pw_sc.Rmd’ using ‘UTF-8’... OK
  ‘tf_bk.Rmd’ using ‘UTF-8’... OK
  ‘tf_sc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.18/2024-03-30_1314/decoupleR/decoupleR.Rcheck/00check.log’
for details.

[ Finished: 2024-03-30 13:38:40 CET ]