Maintainer: ‘Junyao Jiang <jiangjunyao789@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Junyao",
                    family = "Jiang",
                    role = c("aut", "cre"),
                    email = "jiangjunyao789@163.com")
as necessary.
Running examples in ‘CACIMAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Running ‘testthat.R’ [17s/22s]
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
Maintainer: ‘Junyao Jiang <jiangjunyao789@163.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Junyao",
                    family = "Jiang",
                    role = c("aut", "cre"),
                    email = "jiangjunyao789@163.com")
as necessary.
Running examples in ‘CACIMAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Running ‘testthat.R’ [10s/13s]
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
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
Running ‘testthat.R’ [25s/43s]
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
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
Running ‘testthat.R’ [25s/37s]
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
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
Running 'testthat.R' [13s]
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
Running examples in ‘CACIMAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Running ‘testthat.R’ [16s/20s]
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
Running examples in ‘CACIMAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Running ‘testthat.R’ [16s/20s]
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
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
Running 'testthat.R' [13s]
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
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
Running 'testthat.R' [18s]
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