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SydneyBioX / spicyR

https://sydneybiox.github.io/spicyR/
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Deprecation warnings #25

Closed alboll-lab closed 1 year ago

alboll-lab commented 1 year ago

Hello,

Thanks a lot for providing the spicyR package, I really value it! I recently wanted to use it on a SingleCellExperiment object and got some deprecation warnings. I was wondering whether these can be safely ignored? I run the code also on the test data from Damond et al 2019 and received the same warning messages (see below). Thanks a lot in advance for your help!

> spicyTestPair <- spicy(
+   diabetesData_SCE,
+   condition = "stage",
+   subject = "case",
+   from = "beta",
+   to = "delta"
+ )

Testing for spatial differences across conditions accounting for multiple images per subject
Warning messages:
1: The dim() method for DataFrameList objects is deprecated. Please use dims() on these objects instead. 
2: The nrow() method for DataFrameList objects is deprecated. Please use nrows() on these objects instead. 
3: The ncol() method for CompressedSplitDataFrameList objects is deprecated. Please use ncols() on these objects instead. 
4: The dim() method for DataFrameList objects is deprecated. Please use dims() on these objects instead. 
5: The nrow() method for DataFrameList objects is deprecated. Please use nrows() on these objects instead. 
6: The ncol() method for CompressedSplitDataFrameList objects is deprecated. Please use ncols() on these objects instead. 

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggplot2_3.4.1               SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 Biobase_2.58.0              GenomicRanges_1.50.2       
 [6] GenomeInfoDb_1.34.9         IRanges_2.32.0              S4Vectors_0.36.2            BiocGenerics_0.44.0         MatrixGenerics_1.10.0      
[11] matrixStats_0.63.0          spicyR_1.10.7               BiocManager_1.30.20
nick-robo commented 1 year ago

Thanks for the issue. This can be safely ignored, but we will try to fix it ASAP.