Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'VDJ_build.R'
Running examples in 'Platypus-Ex.R' failed
The error most likely occurred in:

> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘VDJ_build.R’
Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'VDJ_build.R'
Running examples in 'Platypus-Ex.R' failed
The error most likely occurred in:

> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted
Running examples in 'Platypus-Ex.R' failed
The error most likely occurred in:

> ### Name: GEX_coexpression_coefficient
> ### Title: Coexpression of selected genes
> ### Aliases: GEX_coexpression_coefficient
> 
> ### ** Examples
> 
> GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
+ , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)
Error:
! The `slot` argument of `FetchData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
    ▆
 1. └─Platypus::GEX_coexpression_coefficient(...)
 2.   ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts")
 3.   └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts")
 4.     └─SeuratObject::.Deprecate(...)
 5.       └─lifecycle::deprecate_stop(...)
 6.         └─lifecycle:::deprecate_stop0(msg)
 7.           └─rlang::cnd_signal(...)
Execution halted