* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/scDiffCom.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 ‘scDiffCom/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDiffCom’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'rrvgo', 'SingleCellSignalR'
* 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 ‘scDiffCom’ can be installed ... [54s/70s] OK
* checking package 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 ... [11s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/16s] OK
* checking whether the package can be unloaded cleanly ... [11s/16s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/16s] OK
* checking loading without being on the library search path ... [11s/14s] 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 ... [72s/92s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* 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 ... OK
* 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 R/sysdata.rda ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’ [321s/228s]
 [322s/229s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(scDiffCom)
  > 
  > test_check("scDiffCom")
  Loading required package: SeuratObject
  Loading required package: sp
  
  Attaching package: 'SeuratObject'
  
  The following object is masked from 'package:base':
  
      intersect
  
  Extracting data from assay 'RNA' and slot 'data' (assuming normalized log1p-transformed data).
  Converting normalized data from log1p-transformed to non-log1p-transformed.
  Input data: 726 genes, 468 cells and 5 cell-types.
  Input ligand-receptor database: 4582 mouse interactions.
  Number of LRIs that match to genes present in the dataset: 1173.
  Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
  Extracting data from assay 'RNA' and slot 'data' (assuming normalized log1p-transformed data).
  Converting normalized data from log1p-transformed to non-log1p-transformed.
  Input data: 726 genes, 468 cells and 5 cell-types.
  Input ligand-receptor database: 4582 mouse interactions.
  Number of LRIs that match to genes present in the dataset: 1173.
  Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
  Total number of potential cell-cell interactions (CCIs): 29325 (5 * 5 * 1173).
  Performing permutation analysis (10 iterations by batches of 1000) on 8952 potential CCIs.
  Performing batch 1 of 1.
  Extracting data from assay 'RNA' and slot 'data' (assuming normalized log1p-transformed data).
  Converting normalized data from log1p-transformed to non-log1p-transformed.
  Input data: 726 genes, 468 cells and 5 cell-types.
  Input ligand-receptor database: 4582 mouse interactions.
  Number of LRIs that match to genes present in the dataset: 1173.
  Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
  Total number of potential cell-cell interactions (CCIs): 29325 (5 * 5 * 1173).
  Performing permutation analysis (1000 iterations by batches of 1000) on 8952 potential CCIs.
  Performing batch 1 of 1.
  Filtering and cleaning 'raw' CCIs.
  Returning 1896 detected CCIs.
  Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_TERMS, KEGG_PWS.
  Successfully returning final scDiffCom object.
  Extracting data from assay 'RNA' and slot 'data' (assuming normalized log1p-transformed data).
  Converting normalized data from log1p-transformed to non-log1p-transformed.
  Input data: 726 genes, 468 cells and 5 cell-types.
  Input ligand-receptor database: 4582 mouse interactions.
  Number of LRIs that match to genes present in the dataset: 1173.
  Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
  Total number of potential cell-cell interactions (CCIs): 29325 (5 * 5 * 1173).
  Performing permutation analysis (1000 iterations by batches of 1000) on 8952 potential CCIs.
  Performing batch 1 of 1.
  Filtering and cleaning 'raw' CCIs.
  Returning 1896 detected CCIs.
  Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_TERMS, KEGG_PWS.
  Successfully returning final scDiffCom object.
  Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_TERMS, KEGG_PWS.
  No over-representation analysis available for the selected parameters.
  No over-representation analysis available for the selected parameters.
  No over-representation analysis available for the selected parameters.
  Filtering and cleaning 'raw' CCIs.
  Returning 2649 detected CCIs.
  Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_TERMS, KEGG_PWS.
  Erasing all previous ORA results: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_TERMS, KEGG_PWS.
  Performing over-representation analysis on the categories: EMITTER_CELLFAMILY.
  Keeping previous ORA results: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_TERMS, KEGG_PWS.
  [ FAIL 2 | WARN 5 | SKIP 0 | PASS 82 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-everything.R:1047:13'): BuildNetwork works and returns a visNetwork object ──
  Error: Package "visNetwork" needed for this function to work.Please install it.
  Backtrace:
       ▆
    1. └─base::lapply(...) at test-everything.R:1041:5
    2.   └─scDiffCom (local) FUN(X[[i]], ...)
    3.     └─base::lapply(...) at test-everything.R:1044:9
    4.       └─scDiffCom (local) FUN(X[[i]], ...)
    5.         ├─testthat::expect_s3_class(...) at test-everything.R:1047:13
    6.         │ └─testthat::quasi_label(enquo(object), arg = "object")
    7.         │   └─rlang::eval_bare(expr, quo_get_env(quo))
    8.         ├─scDiffCom::BuildNetwork(...)
    9.         └─scDiffCom::BuildNetwork(...)
   10.           └─scDiffCom:::build_interactive_network(...)
  ── Error ('test-everything.R:1064:1'): (code run outside of `test_that()`) ─────
  Error: Package "visNetwork" needed for this function to work.Please install it.
  Backtrace:
      ▆
   1. └─scDiffCom:::build_interactive_network(...) at test-everything.R:1064:1
  
  [ FAIL 2 | WARN 5 | SKIP 0 | PASS 82 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... 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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/scDiffCom.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 11:36.90, 659.12 + 37.58