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Added details in README.md on 'RMariaDB issue'
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Maurits Evers committed Sep 12, 2019
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Expand Up @@ -27,7 +27,7 @@ This is production code! Use it at your own risk. That means that documentation

Due to some substantial changes in functions/methods from some R/Bioconductor packages that RNAModR depends on, RNAModR's functionality is currently limited. Specifically,

1. `BuildTx` (building a custom reference transcriptome) is broken (but you can still use the pre-generated transcriptomes from the links below); this seems to be related to major [changes in `GenomicRanges` version 1.32.0](https://github.com/Bioconductor/GenomicRanges/blob/master/NEWS), which
1. `BuildTx` (building a custom reference transcriptome) is broken (but you can still use the pre-generated transcriptomes from the links below); this seems to be related to major [changes in `GenomicRanges` version 1.32.0](https://github.com/Bioconductor/GenomicRanges/blob/master/NEWS) and changes in `RMariaDB` that completely [break functionality of `GenomicFeatures::makeTxDbFromUCSC`](https://github.com/r-dbi/RMariaDB/issues/135) (verified on MacOS Sierra). I am unsure how badly other OS are affected. A workaround/fix for MacOS Sierra (that should also work for other flavours) has been posted as part of [Issue #5](https://github.com/mevers/RNAModR/issues/5).
2. `plotRelDistDistribution` and `plotRelDistEnrichment()` are broken; this is related to afore-mentioned changes in `GenomicRanges`, which introduced a `CompressedGRangesList` class as a replacement for the `GRangesList` class.

I appreciate any and all testing; for issues, please open an official [Issue](https://github.com/mevers/RNAModR/issues/new) on the GitHub project site.
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