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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in unlist(., .data, use.names = FALSE) : 
  'recursive' must be a length-1 vector
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown

Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Example_RT_distribution.Rmd’

--- re-building ‘Requirements.Rmd’ using rmarkdown
--- finished re-building ‘Requirements.Rmd’

--- re-building ‘Workflow.Rmd’ using rmarkdown

Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in unlist(., .data, use.names = FALSE) : 
  'recursive' must be a length-1 vector
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown

Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Example_RT_distribution.Rmd’

--- re-building ‘Requirements.Rmd’ using rmarkdown
--- finished re-building ‘Requirements.Rmd’

--- re-building ‘Workflow.Rmd’ using rmarkdown

Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’

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

> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in unlist(., .data, use.names = FALSE) : 
  'recursive' must be a length-1 vector
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown

Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Example_RT_distribution.Rmd’

--- re-building ‘Requirements.Rmd’ using rmarkdown
--- finished re-building ‘Requirements.Rmd’

--- re-building ‘Workflow.Rmd’ using rmarkdown

Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’

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

> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in unlist(., .data, use.names = FALSE) : 
  'recursive' must be a length-1 vector
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Example_RT_distribution.Rmd’ using rmarkdown

Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Example_RT_distribution.Rmd’

--- re-building ‘Requirements.Rmd’ using rmarkdown
--- finished re-building ‘Requirements.Rmd’

--- re-building ‘Workflow.Rmd’ using rmarkdown

Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building ‘Workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘Example_RT_distribution.Rmd’ ‘Workflow.Rmd’

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

> ### Name: convert_all_levels
> ### Title: Conversion of software specific levels
> ### Aliases: convert_all_levels
> 
> ### ** Examples
> 
> # Load libraries
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> library(stringr)
> library(tidyr)
> library(comprehenr)
> library(tibble)
> 
> # MaxQuant example data
> evidence <- tibble::tibble(
+   "Modified sequence" = c("_AACLLPK_",
+    "_ALTDM(Oxidation (M))PQM(Oxidation (M))R_",
+    "ALTDM(Dummy_Modification)PQMK"),
+   Charge = c(2,2,3),
+   "Protein group IDs" = c("26", "86;17", "86;17")
+ )
> 
> proteingroups <- tibble::tibble(
+ "Protein IDs" = c("A0A075B6P5;P01615;A0A087WW87;P01614;A0A075B6S6", "P02671", "P02672"),
+ id = c(26, 86, 17)
+ )
> 
> # Conversion
> convert_all_levels(
+  input_df = evidence,
+  input_MQ_pg = proteingroups,
+  software = "MaxQuant"
+ )
Error in unlist(., .data, use.names = FALSE) : 
  'recursive' must be a length-1 vector
Calls: convert_all_levels -> sort_string_pg -> %>% -> unlist
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Example_RT_distribution.Rmd' using rmarkdown

Quitting from lines 51-55 [all levels] (Example_RT_distribution.Rmd)
Error: processing vignette 'Example_RT_distribution.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building 'Example_RT_distribution.Rmd'

--- re-building 'Requirements.Rmd' using rmarkdown
--- finished re-building 'Requirements.Rmd'

--- re-building 'Workflow.Rmd' using rmarkdown

Quitting from lines 97-101 [proteinGroup] (Workflow.Rmd)
Error: processing vignette 'Workflow.Rmd' failed with diagnostics:
'recursive' must be a length-1 vector
--- failed re-building 'Workflow.Rmd'

SUMMARY: processing the following files failed:
  'Example_RT_distribution.Rmd' 'Workflow.Rmd'

Error: Vignette re-building failed.
Execution halted