R Under development (unstable) (2024-07-02 r86866 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(ssdGSA)


> 
> test_check("ssdGSA")
Warning messages: 
100% (10/10) of gene sets have information missing in the data matrix for at least one gene; 
50% (5/10) of gene sets have information missing in the direction matrix for at least one gene. 

Note since more than 10 gene sets have missing information in the data matrix, no detailed individual gene set missing information will be reported.
MAPK.KEGG_MAPK_SIGNALING_PATHWAY: 
 0.75% of genes (2/267) in this gene set have information missing in the direction matrix; 

CALCIUM.KEGG_CALCIUM_SIGNALING_PATHWAY: 
 0.56% of genes (1/178) in this gene set have information missing in the direction matrix; 

CHEMOKINE.KEGG_CHEMOKINE_SIGNALING_PATHWAY: 
 1.05% of genes (2/190) in this gene set have information missing in the direction matrix; 

GNRH.KEGG_GNRH_SIGNALING_PATHWAY: 
 0.99% of genes (1/101) in this gene set have information missing in the direction matrix; 

VEGF.KEGG_VEGF_SIGNALING_PATHWAY: 
 1.32% of genes (1/76) in this gene set have information missing in the direction matrix; 

Note: Running GSA for 10 gene sets using 'gsva' method with 'group_weighted' weights.
Warning messages: 
100% (10/10) of gene sets have information missing in the data matrix for at least one gene; 
50% (5/10) of gene sets have information missing in the direction matrix for at least one gene. 

Note since more than 10 gene sets have missing information in the data matrix, no detailed individual gene set missing information will be reported.
MAPK.KEGG_MAPK_SIGNALING_PATHWAY: 
 0.75% of genes (2/267) in this gene set have information missing in the direction matrix; 

CALCIUM.KEGG_CALCIUM_SIGNALING_PATHWAY: 
 0.56% of genes (1/178) in this gene set have information missing in the direction matrix; 

CHEMOKINE.KEGG_CHEMOKINE_SIGNALING_PATHWAY: 
 1.05% of genes (2/190) in this gene set have information missing in the direction matrix; 

GNRH.KEGG_GNRH_SIGNALING_PATHWAY: 
 0.99% of genes (1/101) in this gene set have information missing in the direction matrix; 

VEGF.KEGG_VEGF_SIGNALING_PATHWAY: 
 1.32% of genes (1/76) in this gene set have information missing in the direction matrix; 

Note: Running GSA for 10 gene sets using individual weights.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-ssdGSA_individual.R:1:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ssdGSA.R:2:3'): ssdGSA works ───────────────────────────────────
<defunctError/error/condition>
Error in `gsva(Data, Gene_sets_pov, method = GSA_method, min.sz = min.sz, 
    max.sz = max.sz, mx.diff = mx.diff)`: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Backtrace:
    ▆
 1. └─ssdGSA::ssdGSA(...) at test-ssdGSA.R:2:3
 2.   ├─base::suppressMessages(...)
 3.   │ └─base::withCallingHandlers(...)
 4.   ├─GSVA::gsva(...)
 5.   └─GSVA::gsva(...)
 6.     └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').")

[ FAIL 1 | WARN 0 | SKIP 1 | PASS 0 ]
Error: Test failures
Execution halted