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Error in data.frame during sql database creation #3

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kaisengit opened this issue Jun 1, 2021 · 0 comments
Open

Error in data.frame during sql database creation #3

kaisengit opened this issue Jun 1, 2021 · 0 comments

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@kaisengit
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After generating the params file, I get the following error when creating the sql database from the Skyline file:

> ### Run AvG
> library(AvantGardeDIA)
> AvantGardeDIA::AvantGardeDIA_InChunks_DB(D.file.name = D.file.name,RefinementWorkflow = "GlobalRefinement")

-- Column specification --------------------------------------------------------
cols(
  .default = col_character(),
  IsDecoy = col_logical(),
  PrecursorCharge = col_double(),
  PrecursorMz = col_double(),
  ProductCharge = col_double(),
  ProductMz = col_double(),
  Quantitative = col_logical(),
  LibraryDotProduct = col_double(),
  MinStartTime = col_double(),
  MaxEndTime = col_double(),
  Area = col_double(),
  LibraryIntensity = col_double()
)
i Use `spec()` for the full column specifications.

Error in data.frame(u, Start_ID_Analyte = unique(D$Data$ID_Analyte)[1],  : 
  arguments imply differing number of rows: 1, 0
Calls: <Anonymous> -> data.frame
In addition: Warning message:
The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
Execution halted

I am running Skyline 21.1.0.146 and installed AvantGarde 0.0.1.5 from the tools store. Note that the AvantGarde R package was not installed automatically and I had to install it manually (R 4.0.3 was installed by Skyline).

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