• using R Under development (unstable) (2025-12-12 r89161)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.7     flang version 21.1.7
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘CACIMAR/DESCRIPTION’ ... OK
• this is package ‘CACIMAR’ version ‘1.0.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘CACIMAR’ can be installed ... [53s/148s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [15s/41s] OK
• checking whether the package can be loaded with stated dependencies ... [14s/34s] OK
• checking whether the package can be unloaded cleanly ... [15s/39s] OK
• checking whether the namespace can be loaded with stated dependencies ... [12s/28s] OK
• checking whether the namespace can be unloaded cleanly ... [13s/36s] OK
• checking loading without being on the library search path ... [14s/38s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [67s/181s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [20s/52s] ERROR Running examples in ‘CACIMAR-Ex.R’ failed The error most likely occurred in: > ### Name: Format_Markers_Frac > ### Title: Format marker genes for plotting > ### Aliases: Format_Markers_Frac > > ### ** Examples > > data("pbmc_small") > all.markers <- Identify_Markers(pbmc_small) Calculating cluster 0 Calculating cluster 1 Calculating cluster 2 [1] "0" 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. └─CACIMAR::Identify_Markers(pbmc_small)   2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)   3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)   4. └─CACIMAR:::Markertest(...)   5. ├─Seurat::GetAssayData(object = object, slot = "data")   6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")   7. └─SeuratObject::.Deprecate(...)   8. └─lifecycle::deprecate_stop(...)   9. └─lifecycle:::deprecate_stop0(msg)  10. └─rlang::cnd_signal(...) Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [29s/83s] ERROR   Running ‘testthat.R’ [28s/81s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(CACIMAR)   Loading required package: Seurat   Loading required package: SeuratObject   Loading required package: sp      Attaching package: 'SeuratObject'      The following objects are masked from 'package:base':          intersect, t      >   > test_check("CACIMAR")      mm_zf_0T1 mm_zf_1T0 mm_zf_1T1 mm_zf_1TN mm_zf_NT1 mm_zf_NTN       14207 37432 10353 3238 273 128   [1] "mm_zf_0T1"   [1] "mm_zf_1T0"   [1] "mm_zf_1T1"   [1] "mm_zf_1TN"   [1] "mm_zf_NT1"   [1] "mm_zf_NTN"   Using NCS as value column: use value.var to override.   Calculating cluster 0   Calculating cluster 1   Calculating cluster 2   [1] "0"   Saving _problems/test-test1-10.R   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-test1.R:10:3'): test CACIMAR ───────────────────────────────────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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. └─CACIMAR::Identify_Markers(pbmc_small) at test-test1.R:10:3     2. └─CACIMAR:::Identify_Markers1(Seurat_object, PowerCutoff, DifferenceCutoff)     3. └─CACIMAR:::Cal_MarkersRoc(Seurat_object, uMarker2)     4. └─CACIMAR:::Markertest(...)     5. ├─Seurat::GetAssayData(object = object, slot = "data")     6. └─SeuratObject:::GetAssayData.Seurat(object = object, slot = "data")     7. └─SeuratObject::.Deprecate(...)     8. └─lifecycle::deprecate_stop(...)     9. └─lifecycle:::deprecate_stop0(msg)    10. └─rlang::cnd_signal(...)      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [7s/22s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs