Thanks for the report. It should be fixed in S4Vectors 0.21.22. On Mon, Apr 1, 2019 at 12:01 PM Ludwig Geistlinger < ludwig.geistlin...@sph.cuny.edu> wrote:
> I have a SummarizedExperiment with putatively user-annoted rowData. > I have a function that does computation on this SE and appends > the results to the rowData. > When (repeatedly) called on the SE, the function just overwrites / > replaces already existing columns. > > In R release and S4Vectors_0.20.1 > > > sessionInfo() > R version 3.5.2 (2018-12-20) > Platform: x86_64-apple-darwin15.6.0 (64-bit) > Running under: macOS Mojave 10.14.3 > > Matrix products: default > BLAS: > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib > LAPACK: > /Library/Frameworks/R.framework/Versions/3.5/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] parallel stats4 stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] S4Vectors_0.20.1 BiocGenerics_0.28.0 > > loaded via a namespace (and not attached): > [1] compiler_3.5.2 > > this works: > > # my rowData > > d <- DataFrame(a=c(1,2), b=c(3,4), c=c(5,6)) > DataFrame with 2 rows and 3 columns > a b c > <numeric> <numeric> <numeric> > 1 1 3 5 > 2 2 4 6 > > # output of my function > > d2 <- DataFrame(b=c(7,8), c=c(9,10), d=c(11,12)) > DataFrame with 2 rows and 3 columns > b c d > <numeric> <numeric> <numeric> > 1 7 9 11 > 2 8 10 12 > > # replace and simultaneously append > > d[,colnames(d2)] <- d2 > > d > DataFrame with 2 rows and 4 columns > a b c d > <numeric> <numeric> <numeric> <numeric> > 1 1 7 9 11 > 2 2 8 10 12 > > > > > However, using R-devel and S4Vectors_0.21.20 > > > sessionInfo() > R Under development (unstable) (2019-01-18 r75994) > Platform: x86_64-apple-darwin18.2.0 (64-bit) > Running under: macOS Mojave 10.14.3 > > Matrix products: default > BLAS: /Users/ludwig/Downloads/R-devel/lib/libRblas.dylib > LAPACK: /Users/ludwig/Downloads/R-devel/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] parallel stats4 stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] S4Vectors_0.21.20 BiocGenerics_0.29.2 > > loaded via a namespace (and not attached): > [1] compiler_3.6.0 > > > The same replacement operation causes an error > > > d[,colnames(d2)] <- d2 > Error in names(x@listData) <- value : > 'names' attribute [3] must be the same length as the vector [1] > > > For data.frame, this still works in R-devel: > > dd <- as.data.frame(d) > > dd2 <- as.data.frame(d2) > > dd[,colnames(dd2)] <- dd2 > > dd > a b c d > 1 1 7 9 11 > 2 2 8 10 12 > > How to best address this issue? > > > -- > Dr. Ludwig Geistlinger > CUNY School of Public Health > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
