• using R Under development (unstable) (2025-12-21 r89216)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘CAESAR.Suite’ version ‘0.2.3’
• package encoding: UTF-8
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• checking whether package ‘CAESAR.Suite’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 21.1.7 (1)’
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• checking examples ... [20s/24s] ERROR Running examples in ‘CAESAR.Suite-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CAESAR.CTDEP > ### Title: Test Cell Type Differentially Enriched Pathways > ### Aliases: CAESAR.CTDEP > > ### ** Examples > > data(toydata) > > seu <- toydata$seu > pathway_list <- toydata$pathway_list > cts <- levels(seu)[1:2] > > enrich.score <- CAESAR.enrich.score(seu, pathway_list) Calculate co-embedding distance... Error: ! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject   5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace:     ▆  1. └─CAESAR.Suite::CAESAR.enrich.score(seu, pathway_list)  2. ├─Seurat::GetAssayData(object = seu, slot = "data", assay = assay.dist)  3. └─SeuratObject:::GetAssayData.Seurat(...)  4. └─SeuratObject::.Deprecate(...)  5. └─lifecycle::deprecate_stop(...)  6. └─lifecycle:::deprecate_stop0(msg)  7. └─rlang::cnd_signal(...) Execution halted
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• DONE

Status: 1 ERROR