Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_geneSets_from_msigdbr.Rd: msigdbr
  plot.mGST.Rd: visOptions, visNetwork
  save_as_xls.Rd: WriteXLS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘massiveGST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_geneSets_from_msigdbr.Rd: msigdbr
  plot.mGST.Rd: visOptions, visNetwork
  save_as_xls.Rd: WriteXLS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘massiveGST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Running examples in ‘massiveGST-Ex.R’ failed
The error most likely occurred in:

> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Running examples in ‘massiveGST-Ex.R’ failed
The error most likely occurred in:

> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_geneSets_from_msigdbr.Rd: msigdbr
  plot.mGST.Rd: visOptions, visNetwork
  save_as_xls.Rd: WriteXLS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in 'massiveGST-Ex.R' failed
The error most likely occurred in:

> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
ERROR: cannot open D:\temp\2025_03_25_01_50_00_18701\RtmpqYsR0p/WriteXLS/1.csv
. No such file or directory

Quitting from vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
    ▆
 1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
 2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
 3.   └─massiveGST:::plot.network(...)
 4.     ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
 5.     └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Rd warning: get_geneSets_from_msigdbr.Rd:28: missing link ‘msigdbr’
  Rd warning: plot.mGST.Rd:29: missing link ‘visOptions’
  Rd warning: plot.mGST.Rd:30: missing link ‘visOptions’
  Rd warning: plot.mGST.Rd:45: missing link ‘visNetwork’
  Rd warning: plot.mGST.Rd:45: missing link ‘visOptions’
  Rd warning: save_as_xls.Rd:20: missing link ‘WriteXLS’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/massiveGST.Rcheck/00install.out’ for details.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_geneSets_from_msigdbr.Rd: msigdbr
  plot.mGST.Rd: visOptions, visNetwork
  save_as_xls.Rd: WriteXLS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in ‘massiveGST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Running examples in ‘massiveGST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Running examples in 'massiveGST-Ex.R' failed
The error most likely occurred in:

> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
ERROR: cannot open D:\temp\2025_03_24_01_50_00_31467\RtmpOwPDKI/WriteXLS/1.csv
. No such file or directory

Quitting from vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
    ▆
 1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
 2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
 3.   └─massiveGST:::plot.network(...)
 4.     ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
 5.     └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'massiveGST-Ex.R' failed
The error most likely occurred in:

> ### Name: massiveORT
> ### Title: A wrapper to fisher.test to get over representation analysis of
> ###   gene sets.
> ### Aliases: massiveORT
> 
> ### ** Examples
> 
> library(massiveGST)
> 
> # get the gene profile
> fname <- system.file("extdata", package="massiveGST")
> fname <- file.path(fname, "pre_ranked_list.txt")
> geneProfile <- get_geneProfile(fname)
> geneList <- names(head(geneProfile, 1000))
> 
> # get the gene-sets
> geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol")
msigdbr: R package version 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
  Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> geneSets <- geneSets[1:250]
> 
> # run the function
> ans <- massiveORT(geneList, geneSets)
greater
Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe),  : 
  row names contain missing values
Calls: massiveORT -> data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
ERROR: cannot open D:\temp\2025_03_24_01_50_00_31467\RtmpOwjiyJ/WriteXLS/1.csv
. No such file or directory

Quitting from vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
    ▆
 1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
 2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
 3.   └─massiveGST:::plot.network(...)
 4.     ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
 5.     └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted