[Bioc-devel] DataFrame conversion

[Ramos Perez, Marcel]

Hi Daniel,

Thanks for posting.

Hervé has asked on the R-devel mailing list:

https://stat.ethz.ch/pipermail/r-devel/2024-March/083265.html

I don't think you will have to do anything in your package.
Once fixed, the messages will go away.

Best regards,

Marcel


On 3/13/24 5:09 PM, Daniel Schulz wrote:

Dear all,

I am maintaining the imcRtools package. Since Monday we have a build error on the development version. Most of the errors are attributed to test functions which fail now and can be attributed to the below problem.
It seems that currently with R 4.4 and Bioconductor 3.19 the following code will throw a warning which it did not in R4.3/Bioconductor 3.18:




x <- S4Vectors::DataFrame(x = c(1,2,4),y=c("A","B","C"))





as.data.frame(x)



  x y

1 1 A

2 2 B

3 4 C

Warning message:

In as.data.frame.numeric(col, optional = optional) :

  Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

I don't really understand what changed in R4.4, Bioconductor 3.19 or S4Vectors that we get these warnings. However, many functions, specifically test functions in our package fail now due to the warning.
Any advice on how to handle this?
Best,
Daniel


--
Daniel Schulz, PhD
Senior Scientist

Bodenmiller Lab
Department of Quantitative Biomedicine & Institute of Molecular Health Sciences
University of Zurich & ETH Z�rich
Winterthurerstrasse 190
8057 Zurich, Switzerland

phone: +41 446356604


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--
Marcel Ramos Pérez
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics and Bioinformatics
Elm & Carlton Streets
Buffalo, New York, 14263


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