R Under development (unstable) (2023-11-02 r85465 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> library(testthat)
> library(scDiffCom)
> 
> test_check("scDiffCom")
Loading required package: SeuratObject
Loading required package: sp

Attaching package: 'SeuratObject'

The following objects are 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 0 | WARN 3 | SKIP 0 | PASS 85 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
 237.76   34.14  266.11