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I was perfectly using bioMart, but it gave an error, I went ahead trying to follow the following thread.

And there were some issues with BiocInstaller::biocLite('grimbough/biomaRt'), namely, I needed to install biocLite("remotes") and then follow the link to solve lgfortran error.

After doing all of that and successfully running BiocInstaller::biocLite('grimbough/biomaRt') I still got the same error:

Error in checkDataset(dataset = dataset, mart = mart) : The given dataset: mmusculus_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.

I am using MacOS High Sierra.

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: 
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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  methods   base     

other attached packages ...

Any suggestions would be greatly appreciated.

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  • $\begingroup$ What was the first bioMart error, and how did you get that error? Why did you install the github (development) version of the package instead of the one in Bioconductor? $\endgroup$
    – llrs
    May 11 '18 at 6:57
  • $\begingroup$ I am not sure why it stopped working, some temporary issue with biomaRt, maybe... I switched back to just biocLite() installation and it started to work. It would still be interesting to make the development version work. $\endgroup$ May 12 '18 at 0:31
  • $\begingroup$ Try posting the problem on Bioconductor support site support.bioconductor.org. $\endgroup$ Jun 11 '18 at 23:16

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