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nmquijada / tormes

Making whole bacterial genome sequencing data analysis easy
GNU General Public License v3.0
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Warning: Ignoring 26 observations #32

Closed alantsangmb closed 4 years ago

alantsangmb commented 4 years ago

I have successfully ran and obtain html results using tormes-1.2.0 Most of the results displayed perfectly in the browser, however some warning messages are shown:

Warning: arrange_() is deprecated as of dplyr 0.7.0.

Please use arrange() instead.

See vignette('programming') for more help

This warning is displayed once every 8 hours.

Call lifecycle::last_warnings() to see where this warning was generated.

Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.

Consider 'structure(list(), *)' instead.

Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.

Consider 'structure(list(), *)' instead.

Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.

Consider 'structure(list(), *)' instead.

Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.

Consider 'structure(list(), *)' instead.

Can they be just ignored? Anything I need to update? Thanks.

biobrad commented 4 years ago

Narciso will tell you definitely... But I have been ignoring these for the last six months with no issues.

On Tue, 22 Sep 2020, 1:28 pm alantsangmb, notifications@github.com wrote:

I have successfully ran and obtain html results using tormes-1.2.0 Most of the results displayed perfectly in the browser, however some warning messages are shown: Warning: arrange_() is deprecated as of dplyr 0.7.0. Please use arrange() instead. See vignette('programming') for more help This warning is displayed once every 8 hours. Call lifecycle::last_warnings() to see where this warning was generated. Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, )' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), )' instead. Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, )' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), )' instead. Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, )' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), )' instead. Warning in structure(if (i %in% npscales()) uniq(d[[i]]) else d[[i]], class = oldClass(x[[i]])): Calling 'structure(NULL, )' is deprecated, as NULL cannot have attributes. Consider 'structure(list(), )' instead.

Can they be just ignored? Anything I need to update? Thanks.

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nmquijada commented 4 years ago

Hi @alantsangmb Yes, those warnings can be ignored as they don't affect the results. It seems that plotly (the R package for creating the interactive plots) has some issues with some deprecated functions: https://github.com/ropensci/plotly/issues/1783 So warnings appear without compromising plotly activity. I hope their developers can solve it soon. Best, Narciso

alantsangmb commented 4 years ago

Thank you! :)