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GseaVis

Implement for 'GSEA' Enrichment Visualization

v0.0.5 · Dec 20, 2022 · MIT + file LICENSE
CRAN GitHub Mirror

Description

Mark your interesting genes on plot and support more parameters to handle your own gene set enrichment analysis plot.

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CRAN Check Status

6 ERROR
8 OK
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r-devel-linux-x86_64-debian-clang ERROR
r-devel-linux-x86_64-debian-gcc ERROR
r-devel-linux-x86_64-fedora-clang ERROR
r-devel-linux-x86_64-fedora-gcc ERROR
r-devel-macos-arm64 ERROR
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 OK
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 ERROR
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (6 non-OK)
ERROR r-devel-linux-x86_64-debian-clang

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
> gseaRes <- readRDS(test_data)
> 
> # all plot
> gseaNb(object = gseaRes,
+       geneSetID = 'GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
+       subPlot = 2)
Error in `map()`:
ℹ In index: 1.
Caused by error in `get()`:
! object 'gseaScores' not found
Backtrace:
     ▆
  1. ├─GseaVis::gseaNb(...)
  2. │ └─purrr::map_df(...)
  3. │   └─purrr::map(.x, .f, ...)
  4. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─GseaVis (local) .f(.x[[i]], ...)
  9. │         ├─gsInfo(object, geneSetID = setid) %>% dplyr::mutate(id = setid)
 10. │         └─GseaVis::gsInfo(object, geneSetID = setid)
 11. │           └─utils::getFromNamespace("gseaScores", "DOSE")
 12. │             └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
ERROR r-devel-linux-x86_64-debian-gcc

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
> gseaRes <- readRDS(test_data)
> 
> # all plot
> gseaNb(object = gseaRes,
+       geneSetID = 'GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
+       subPlot = 2)
Error in `map()`:
ℹ In index: 1.
Caused by error in `get()`:
! object 'gseaScores' not found
Backtrace:
     ▆
  1. ├─GseaVis::gseaNb(...)
  2. │ └─purrr::map_df(...)
  3. │   └─purrr::map(.x, .f, ...)
  4. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─GseaVis (local) .f(.x[[i]], ...)
  9. │         ├─gsInfo(object, geneSetID = setid) %>% dplyr::mutate(id = setid)
 10. │         └─GseaVis::gsInfo(object, geneSetID = setid)
 11. │           └─utils::getFromNamespace("gseaScores", "DOSE")
 12. │             └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
ERROR r-devel-linux-x86_64-fedora-clang

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
> gseaRes <- readRDS(test_data)
> 
> # all plot
> gseaNb(object = gseaRes,
+       geneSetID = 'GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
+       subPlot = 2)
Error in `map()`:
ℹ In index: 1.
Caused by error in `get()`:
! object 'gseaScores' not found
Backtrace:
     ▆
  1. ├─GseaVis::gseaNb(...)
  2. │ └─purrr::map_df(...)
  3. │   └─purrr::map(.x, .f, ...)
  4. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─GseaVis (local) .f(.x[[i]], ...)
  9. │         ├─gsInfo(object, geneSetID = setid) %>% dplyr::mutate(id = setid)
 10. │         └─GseaVis::gsInfo(object, geneSetID = setid)
 11. │           └─utils::getFromNamespace("gseaScores", "DOSE")
 12. │             └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
ERROR r-devel-linux-x86_64-fedora-gcc

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
> gseaRes <- readRDS(test_data)
> 
> # all plot
> gseaNb(object = gseaRes,
+       geneSetID = 'GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
+       subPlot = 2)
Error in `map()`:
ℹ In index: 1.
Caused by error in `get()`:
! object 'gseaScores' not found
Backtrace:
     ▆
  1. ├─GseaVis::gseaNb(...)
  2. │ └─purrr::map_df(...)
  3. │   └─purrr::map(.x, .f, ...)
  4. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─GseaVis (local) .f(.x[[i]], ...)
  9. │         ├─gsInfo(object, geneSetID = setid) %>% dplyr::mutate(id = setid)
 10. │         └─GseaVis::gsInfo(object, geneSetID = setid)
 11. │           └─utils::getFromNamespace("gseaScores", "DOSE")
 12. │             └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
ERROR r-devel-macos-arm64

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
> gseaRes <- readRDS(test_data)
> 
> # all plot
> gseaNb(object = gseaRes,
+       geneSetID = 'GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
+       subPlot = 2)
Error in `map()`:
ℹ In index: 1.
Caused by error in `get()`:
! object 'gseaScores' not found
Backtrace:
     ▆
  1. ├─GseaVis::gseaNb(...)
  2. │ └─purrr::map_df(...)
  3. │   └─purrr::map(.x, .f, ...)
  4. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─GseaVis (local) .f(.x[[i]], ...)
  9. │         ├─gsInfo(object, geneSetID = setid) %>% dplyr::mutate(id = setid)
 10. │         └─GseaVis::gsInfo(object, geneSetID = setid)
 11. │           └─utils::getFromNamespace("gseaScores", "DOSE")
 12. │             └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
ERROR r-patched-linux-x86_64

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
> gseaRes <- readRDS(test_data)
> 
> # all plot
> gseaNb(object = gseaRes,
+       geneSetID = 'GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
+       subPlot = 2)
Error in `map()`:
ℹ In index: 1.
Caused by error in `get()`:
! object 'gseaScores' not found
Backtrace:
     ▆
  1. ├─GseaVis::gseaNb(...)
  2. │ └─purrr::map_df(...)
  3. │   └─purrr::map(.x, .f, ...)
  4. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─GseaVis (local) .f(.x[[i]], ...)
  9. │         ├─gsInfo(object, geneSetID = setid) %>% dplyr::mutate(id = setid)
 10. │         └─GseaVis::gsInfo(object, geneSetID = setid)
 11. │           └─utils::getFromNamespace("gseaScores", "DOSE")
 12. │             └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted

Check History

ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 10, 2026
ERROR r-devel-linux-x86_64-debian-gcc

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- 
...[truncated]...
     └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
ERROR r-devel-linux-x86_64-fedora-clang

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
...[truncated]...
     └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted
ERROR r-devel-linux-x86_64-fedora-gcc

examples

Running examples in ‘GseaVis-Ex.R’ failed
The error most likely occurred in:

> ### Name: gseaNb
> ### Title: gseaNb
> ### Aliases: gseaNb
> 
> ### ** Examples
> 
> # load data
> test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
...[truncated]...
     └─base::get(x, envir = ns, inherits = FALSE)
 13. ├─dplyr::mutate(., id = setid)
 14. └─base::.handleSimpleError(...)
 15.   └─purrr (local) h(simpleError(msg, call))
 16.     └─cli::cli_abort(...)
 17.       └─rlang::abort(...)
Execution halted

Dependency Network

Dependencies Reverse dependencies aplot DOSE dplyr ggplot2 ggpp ggrepel ggsci magrittr purrr RColorBrewer reshape2 stringr tibble GseaVis

Version History

new 0.0.5 Mar 10, 2026