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dev UD - #28

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vertesy wants to merge 26 commits into
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Open

dev UD#28
vertesy wants to merge 26 commits into
devfrom
main

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@vertesy

@vertesy vertesy commented Aug 28, 2026

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@vertesy

vertesy commented Aug 28, 2026

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@copilot
1 resolve the merge conflicts in this pull request
2 Go through the merge and make sure that we are not introducing any retrograde or regressive change. Also, make sure that we do not introduce problems that have been fixed on the development branch.

Copilot AI commented Aug 28, 2026

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@vertesy I can’t apply these changes because the pull request’s branch is the repository’s default branch, which I’m not allowed to push to directly.

You can ask me to create a new pull request with the requested changes instead and I'll open a separate PR on a new branch.

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💡 Codex Review

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Reviewed commit: a6e50c876d

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Comment thread R/ReadWriter.R
read_in <- as.data.frame(gtools::na.replace(read_in, replace = 0))
}

if (wRownames) read_in <- column.2.row.names(read_in, as_df = !asTibble)

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P1 Badge Remove the undefined asTibble lookup

With the default wRownames = TRUE, every successful SSV read evaluates !asTibble, but read.simple.ssv() neither declares that parameter nor defines the variable. Normal callers therefore get object 'asTibble' not found instead of their data; add the parameter explicitly or retain the previous data-frame conversion behavior.

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Comment thread R/ReadWriter.R
manual_directory = manual_directory
)

dir.create(dirname(FnP), recursive = TRUE, showWarnings = FALSE)

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P2 Badge Create the target directory before validating it

When manual_directory names a directory that does not exist yet, construct.file.path() now stops at its dir.exists(out_dir) assertion, so execution can never reach this recursive dir.create() call. Create the directory before constructing the path, or allow the constructor to return paths under not-yet-created directories.

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Comment thread R/ReadWriter.R
Comment on lines 717 to 719
write.simple.vec <- function(input_vec, filename = substitute(input_vec), suffix = NULL, extension = "vec",
manual_file_name = NULL, manual_directory = NULL, o = FALSE,
make_names = TRUE, manual_file_name = NULL, manual_directory = NULL, o = FALSE,
v = TRUE) {

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P2 Badge Preserve positional order when adding make_names

Existing callers that pass manual_file_name as the fifth positional argument now bind that filename to make_names; the subsequent if (make_names) then receives a character value and errors. Add the new option after the existing parameters so the established positional API continues to work.

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Comment thread R/ReadWriter.R
Comment on lines +936 to +937
o = FALSE, gzip = FALSE,
TabColor = "darkgoldenrod1", HeaderLineColor = "darkolivegreen3",

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P2 Badge Preserve positional order when adding gzip

For existing positional calls, the eighth argument previously configured TabColor but now binds to gzip, while every later styling argument is shifted as well. A color string ultimately reaches if (gzip) and causes an error after writing the workbook; append the new option after the existing arguments or otherwise preserve their positions.

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2 participants