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List:       bioc-devel
Subject:    Re: [Bioc-devel] DataFrame conversion
From:       "Ramos Perez, Marcel via Bioc-devel" <bioc-devel () r-project ! org>
Date:       2024-03-13 21:18:11
Message-ID: 5308e2c9-a311-4471-ab7c-07b24a1aeb1a () roswellpark ! org
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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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