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> library(testthat)
> library(rliger)
Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions.

We recommand you backup your old analysis before overwriting any existing result.

`readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure.
> 
> test_check("rliger")
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Reading input file...

Number of nodes: 600
Number of edges: 18017

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Modularity: 0.7390
Number of communities: 8
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Reading input file...

Number of nodes: 600
Number of edges: 17528

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Modularity: 0.7567
Number of communities: 8
Elapsed time: 0 seconds
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Wilcoxon rank-sum test over 266 features across 300 cells
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Wilcoxon rank-sum test over 249 features across 600 cells
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 49910.7
UINMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 4377.62
UINMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 4629.63
UINMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 11026.4
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   45414.7
**|
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 41528.3
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 47418.4
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 45693.4
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 45973.6
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 22149.3
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 66227.2
INMF started, niter=2
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 66117.9
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   37129
**|
Starting online iNMF scenario 2, update factorization with new datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**********************************************Total iterations:  15
Total time:        0 sec
Objective error:   54366.5
****|
Starting online iNMF scenario 2, update factorization with new datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**********************************************Total iterations:  15
Total time:        0 sec
Objective error:   54366.5
****|
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   37129
**|
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   37129
**|
INMF started, niter=30
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Total time:      0 sec
Objective error: 35967.3
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   45414.7
**|
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
A liger command record, performed at 05-01-2025 12:41:02 EDT 
Call: normalize.liger(object) 
Parameters:
    useDatasets : "ctrl", "stim" 
    verbose : TRUE 
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   45414.7
**|
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Working ctrl H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\ctrltest_29a1864ae729c.h5 
Working stim H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\stimtest_29a187cfb4c93.h5 
Working ctrl H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\ctrltest_29a1824ae7b3a.h5 
Working stim H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\stimtest_29a1876c95bb2.h5 
Working ctrl H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\ctrltest_29a186688c.h5 
Working stim H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\stimtest_29a1835867d28.h5 
Working ctrl H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\ctrltest_29a1827c25eb.h5 
Working stim H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\stimtest_29a18117577f6.h5 
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   37129
**|
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Working ctrl H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\ctrltest_29a18210249f1.h5 
Working stim H5 file path:  D:\temp\2025_05_01_18_30_17_25507\RtmpYlr5C8\stimtest_29a1826b8d9.h5 
Starting online iNMF scenario 1, factorize all datasets
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
************************************************Total iterations:  30
Total time:        0 sec
Objective error:   37129
**|
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

[ FAIL 0 | WARN 0 | SKIP 18 | PASS 1235 ]

══ Skipped tests (18) ══════════════════════════════════════════════════════════
• On CRAN (11): 'test_downstream.R:83:5', 'test_downstream.R:152:5',
  'test_downstream.R:190:5', 'test_downstream.R:283:5',
  'test_downstream.R:308:5', 'test_factorization.R:232:5',
  'test_factorization.R:264:5', 'test_factorization.R:299:5',
  'test_object.R:390:5', 'test_object.R:443:5', 'test_object.R:530:5'
• Skipping (6): 'test_object.R:68:5', 'test_object.R:321:5',
  'test_preprocessing.R:41:13', 'test_preprocessing.R:153:13',
  'test_preprocessing.R:218:13', 'test_preprocessing.R:285:13'
• {fields} is not installed (1): 'test_preprocessing.R:94:5'

[ FAIL 0 | WARN 0 | SKIP 18 | PASS 1235 ]
> 
> proc.time()
   user  system elapsed 
  97.43    3.35  123.25