metadata items names change in 1.17.6

[mcjmigdal]

Hi,

I see that your build are failing, but wanted to report an issue that appeared for me in version 1.17.6. Note that I am using R 4.1.0.

> library("MultiAssayExperiment")
> names(metadata(miniACC))
[1] "metadata.title"              "metadata.PMID"              
[3] "metadata.sourceURL"  "metadata.RPPAfeatureDataURL"
[5] "metadata.colDataExtrasURL"

As you can see metadata's item names have "metadata." prefix.

Also adding new item to metadata does some unexpected thing with item names.

metadata(miniACC)[["foo"]] <- "bar"
> names(metadata(miniACC))
[1] "metadata.metadata.title"             
[2] "metadata.metadata.PMID"              
[3] "metadata.metadata.sourceURL"         
[4] "metadata.metadata.RPPAfeatureDataURL"
[5] "metadata.metadata.colDataExtrasURL"  
[6] "metadata.foo"

Sorry for not attaching sessionInfo, I have some issue copying it's output.

Hope this helps!

[vjcitn]

confirmed with

names(metadata(miniACC)) [1] "metadata.title" "metadata.PMID" [3] "metadata.sourceURL" "metadata.RPPAfeatureDataURL" [5] "metadata.colDataExtrasURL" sessionInfo() R Under development (unstable) (2020-12-08 r79595) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS (fossa-melisa X20)

Matrix products: default BLAS: /home/stvjc/R-dev-dist/lib/R/lib/libRblas.so LAPACK: /home/stvjc/R-dev-dist/lib/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] MultiAssayExperiment_1.17.6 SummarizedExperiment_1.21.1 [3] Biobase_2.51.0 GenomicRanges_1.43.3 [5] GenomeInfoDb_1.27.3 IRanges_2.25.6 [7] S4Vectors_0.29.6 BiocGenerics_0.37.0 [9] MatrixGenerics_1.3.0 matrixStats_0.57.0 [11] rmarkdown_2.6

loaded via a namespace (and not attached): [1] knitr_1.30 XVector_0.31.1 zlibbioc_1.37.0 [4] lattice_0.20-41 rlang_0.4.10 tools_4.1.0 [7] grid_4.1.0 xfun_0.20 htmltools_0.5.1 [10] digest_0.6.27 startup_0.15.0 Matrix_1.3-2 [13] GenomeInfoDbData_1.2.4 bitops_1.0-6 RCurl_1.98-1.2 [16] evaluate_0.14 DelayedArray_0.17.7 compiler_4.1.0

On Mon, Jan 18, 2021 at 6:28 AM Migdal notifications@github.com wrote:

Hi,

I see that your build are failing, but wanted to report an issue that appeared for me in version 1.17.6. Note that I am using R 4.1.0.

`

library("MultiAssayExperiment") names(metadata(miniACC)) [1] "metadata.title" "metadata.PMID" [3] "metadata.sourceURL" "metadata.RPPAfeatureDataURL" [5] "metadata.colDataExtrasURL" As you can see metadata's item names have"metadata."` prefix.

Also adding new item to metadata does some unexpected thing with item names. ` metadata(miniACC)[["foo"]] <- "bar"

names(metadata(miniACC)) [1] "metadata.metadata.title" [2] "metadata.metadata.PMID" [3] "metadata.metadata.sourceURL" [4] "metadata.metadata.RPPAfeatureDataURL" [5] "metadata.metadata.colDataExtrasURL" [6] "metadata.foo" `

Sorry for not attaching sessionInfo, I have some issue copying it's output.

Hope this helps!

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[LiNk-NY]

Thanks for reporting @mcjmigdal This should be resolved in ad91317 1.17.7 Best, Marcel cc: @vjcitn