R Under development (unstable) (2025-10-13 r88918 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scDiffCom)
> 
> test_check("scDiffCom")
Loading required namespace: SeuratObject
Extracting data from assay 'RNA' and layer '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 layer '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 layer '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 layer '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.
Using custom LRI table. Use at your own risk!
Extracting data from assay 'RNA' and layer '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.
Using custom LRI table. Use at your own risk!
Extracting data from assay 'RNA' and layer '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: 500 custom interactions.
Number of LRIs that match to genes present in the dataset: 83.
Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
Total number of potential cell-cell interactions (CCIs): 2075 (5 * 5 * 83).
Performing permutation analysis (1000 iterations by batches of 1000) on 883 potential CCIs.
Performing batch 1 of 1.
Filtering and cleaning 'raw' CCIs.
Returning 149 detected CCIs.
ORA not performed on GO/KEGG when using a custom LRI database, unless custom tables are provided.
Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE.
Successfully returning final scDiffCom object.
Using custom LRI table. Use at your own risk!
Extracting data from assay 'RNA' and layer '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: 500 custom interactions.
Number of LRIs that match to genes present in the dataset: 83.
Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
Total number of potential cell-cell interactions (CCIs): 2075 (5 * 5 * 83).
Performing permutation analysis (1000 iterations by batches of 1000) on 883 potential CCIs.
Performing batch 1 of 1.
Filtering and cleaning 'raw' CCIs.
Returning 149 detected CCIs.
ORA not performed on GO/KEGG when using a custom LRI database, unless custom tables are provided.
Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE.
Successfully returning final scDiffCom object.
Using custom LRI table. Use at your own risk!
Extracting data from assay 'RNA' and layer '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: 500 custom interactions.
Number of LRIs that match to genes present in the dataset: 83.
Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
Total number of potential cell-cell interactions (CCIs): 2075 (5 * 5 * 83).
Performing permutation analysis (1000 iterations by batches of 1000) on 883 potential CCIs.
Performing batch 1 of 1.
Filtering and cleaning 'raw' CCIs.
Returning 149 detected CCIs.
ORA not performed on GO/KEGG when using a custom LRI database, unless custom tables are provided.
Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_ID.
Successfully returning final scDiffCom object.
Using custom LRI table. Use at your own risk!
Extracting data from assay 'RNA' and layer '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: 500 custom interactions.
Number of LRIs that match to genes present in the dataset: 83.
Type of analysis to be performed: differential analysis between YOUNG and OLD cells.
Total number of potential cell-cell interactions (CCIs): 2075 (5 * 5 * 83).
Performing permutation analysis (1000 iterations by batches of 1000) on 883 potential CCIs.
Performing batch 1 of 1.
Filtering and cleaning 'raw' CCIs.
Returning 149 detected CCIs.
ORA not performed on GO/KEGG when using a custom LRI database, unless custom tables are provided.
Performing over-representation analysis on the categories: LRI, LIGAND_COMPLEX, RECEPTOR_COMPLEX, ER_CELLTYPES, EMITTER_CELLTYPE, RECEIVER_CELLTYPE, GO_ID.
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 0 | WARN 0 | SKIP 0 | PASS 91 ]
> 
> proc.time()
   user  system elapsed 
 444.18   53.17  493.82