Debugging

[jennahamlin]

Error when using clade annotator in Tinsel on CDC server

This is not a problem on my mac

Error message from CDC log file:

Warning: Error in : Assigned data `values` must be compatible with existing data.
ℹ Error occurred for column `2013C-3134`.
✖ Can't convert <double> to <character>.
  362: <Anonymous>

This error appears like it might be associated with the vctrs package

Checking for reproducible error in Rstudio

install.packages("vctrs")
library(vctrs)

> vec_cast(1, integer())
[1] 1

> vec_cast(1, character())
Error: Can't convert <double> to <character>.
Run `rlang::last_error()` to see where the error occurred.
> rlang::last_error()
<error/vctrs_error_incompatible_type>
Can't convert <double> to <character>.
Backtrace:
 1. vctrs::vec_cast(1, character())
 2. vctrs::vec_default_cast(...)
 3. vctrs::stop_incompatible_cast(...)
 4. vctrs::stop_incompatible_type(...)
 5. vctrs:::stop_incompatible(...)
 6. vctrs:::stop_vctrs(...)
Run `rlang::last_trace()` to see the full context.

vec_cast(1, as.numeric(character()))
[1] 1

[jennahamlin]

or is it a problem with reader::redelim

potential alternative r scripting to input into tinsel module to check if it is an reader problem didn't get this to work in r shiny modules, yet

dataFile <- read.delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_geneticMatrix.tsv",
                       sep = "\t",
                       strip.white = T,
                       blank.lines.skip=T,
                       header = F,
                       stringsAsFactors = F
                       )

names(dataFile)<- dataFile[1,]
dataFile <- dataFile[-1,]                
dataFile <- Filter(function(x)!all(is.na(x)), dataFile)

metaFile<-read.delim("/Users/jennahamlin/Desktop/Tinsel/data/example_1504MLEXH-1/1504MLEXH-1_metaData.csv",
                     sep = ",",
                     strip.white = T,
                     blank.lines.skip=T,
                     header = F,
                     stringsAsFactors = F)

names(metaFile) <- metaFile[1,]
metaFile <- metaFile[-1,]

colnames(dataFile)[2:ncol(dataFile)] = metaFile$Display.labels[which(metaFile$Tip.labels %in% colnames(dataFile)[2:ncol(dataFile)])]
dataFile$. = metaFile$Display.labels[which(metaFile$Tip.labels %in% dataFile$.)]

[jennahamlin]

checked if file parsing error was problem for annotation function on cdc instance of tinse

I confirmed that there was an extra tab (\t) in one of the genetic distance test matrix files (1504..) and removed this by hand using text wrangling (show invisible), I used this file as the upload on the cdc server instance of tinsel and the same error occurred when using the annotation function.

I believe that trim_ws =T using reader should have removed this extra column due to the tab at the end of each line; however, it doesn't appear to be doing that. I will post as an issue on readr github.

Posted issue on readr github

[jennahamlin]

error on cdc server ("✖ Can't convert to .") - resolved

Was a result of a different package version for tibble. On my local machine, I was using. 2.1.3 and on the server 3.0.1 was installed. With tibble package version on cdc server now set to 2.1.3, the problem is resolved.

[jennahamlin]

[[: subscript out of bounds

The error occurs when downloading. The above error occurs if the user does this order of operations:

• upload tree, upload genetic distance matrix, annotates tree with one annotation, removes that annotation, and attempts to download

[jennahamlin]

Warning in df$parent == node : longer object length is not a multiple of shorter object length

The order of operations to result in the error is as so:

• upload tree, upload genetic distance matrix, annotate tree with multiple annotations (e.g. 3), remove two annotations and on the removal of the third annotation the error is produced and the application grays out resulting. see pic below

[jennahamlin]

Error message - Error in if: missing value where TRUE/FALSE needed

Order of operations which produces an error that is uninformative for the user:

tree upload, genetic distance upload, add annotation is selected, then meta data is upload for tip label correction

When this happens, then the above error is produces