Why SPADE package has been removed from bioconductor?
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@anhorvath-15868
Last seen 4.0 years ago

Hello everyone,

I would like to use spanning-tree progression analysis of density normalized event (SPADE).

I really think spade tree offers a visualization that helps interpretation.

It seems like bioconductor is the only one that give to us a way to get spade trees in R.

For some reasons, Bioconductors 3.4 removed spade package. I did not find any explanation about that.

I assume that is why I get this error:

> biocLite("spade")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘spade’
Old packages: 'dendextend', 'dplyr', 'FactoMineR', 'graph', 'MASS', 'quantable', 'Rcpp', 'shiny', 'stringi', 'survival', 'tidyr'
Update all/some/none? [a/s/n]: 
n
Warning message:
package ‘spade’ is not available (for R version 3.5.0) 

 

I have found only old comments like everybody forgot about SPADE.

Is that possible to download it directly from http://www.bioconductor.org/packages//2.12/bioc/html/spade.html ?

If so, the reason is missing, still. I do not want my analysis to be wrong because of a defective package.

Thank you very much for all that try to help.

spade release remove clustering • 813 views
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@james-w-macdonald-5106
Last seen 16 hours ago
United States

That package was removed in Bioc3.4, after being deprecated in 3.3 (scroll all the way to the bottom). Packages get deprecated and removed mainly for one of two reasons; either because the maintainer directly states that (s)he no longer desires to maintain the package, and cannot find anybody to take over, or the maintainer abandons the package and it consistently fails in some way. But either way, there no longer appears to be anybody interested in maintaining the package, so it has been removed.

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Thank you for your quick answer. It seems like I will have to abandon that data representation. 

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That's one option. The other obvious option would be to take over maintenance of the package, which might be reasonable if you have a particular need for that data representation. Or you could just install the old version and see if it works for you.

But for either of those options you will be +/- on  your own. We don't offer support for old packages that are no longer maintained. And while there is support on the Bioc-devel listserv for developers, that is usually limited to more high level questions. The expectation for maintainers is that they know what they are doing (and certainly that they know the most of anybody about their own package).

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Ok, it is good to be aware of these potential problems. I will try it and see if it works and if I can understand what's behind. Thank you, problem solved.

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