Question: Why SPADE package has been removed from bioconductor?
0
gravatar for a.n.horvath
17 months ago by
a.n.horvath0 wrote:

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.

clustering spade release remove • 403 views
ADD COMMENTlink modified 17 months ago by James W. MacDonald51k • written 17 months ago by a.n.horvath0
Answer: Why SPADE package has been removed from bioconductor?
0
gravatar for James W. MacDonald
17 months ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 17 months ago by James W. MacDonald51k

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

ADD REPLYlink written 17 months ago by a.n.horvath0

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).

ADD REPLYlink written 17 months ago by James W. MacDonald51k

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.

ADD REPLYlink written 17 months ago by a.n.horvath0
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