[Bioc-devel] Package impute exist in quite different version on CRAN and BioC

[Henrik Bengtsson]

[CC:ing package maintainer of 'impute' package and crossposting to
r-devel and bioc-devel because this affects both audiences]

Hi,

the 'impute' package is published both on CRAN and Bioconductor;

 http://cran.r-project.org/web/packages/impute/
 http://bioconductor.org/packages/2.3/bioc/html/impute.html

The one on CRAN is v1.0-5, and the one on BioC is v1.14.0.

The two different versions of impute.knn() returns different structures, e.g.

impute v1.0-5:
> library(impute)
> example(impute.knn)
> str(khan.imputed)
 num [1:2308, 1:63] 0.773 -2.438 -0.483 -2.721 -1.217 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:2308] "2" "3" "4" "5" ...
  ..$ : chr [1:63] "sample1" "sample2" "sample3" "sample4" ...
 - attr(*, "rng.seed")= num 3.62e+08
 - attr(*, "rng.state")= int [1:626] 403 624 1638542565 108172386 -1884566405 -1
838154368 -250773631 919185230 -1001918601 -1002779316 ...

impute v1.14.0:
> library(impute)
> example(impute.knn)
> str(khan.imputed)
List of 3
 $ data     : num [1:2308, 1:63] 0.773 -2.438 -0.483 -2.721 -1.217 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:2308] "2" "3" "4" "5" ...
  .. ..$ : chr [1:63] "sample1" "sample2" "sample3" "sample4" ...
 $ rng.seed : num 3.62e+08
 $ rng.state: int [1:626] 403 624 1638542565 108172386 -1884566405 -1838154368 -
250773631 919185230 -1001918601 -1002779316 ...

This caused me and my collaborators quite a bit of confusion, because
we both were sure we had the latest version installed.  I've located
at least one other case related to this issue, cf. Thread '[R] Help
with impute.knn' on Oct 30, 2008:

   https://stat.ethz.ch/pipermail/r-help/2008-October/178390.html

(People in that thread are also CC:ed, because it was never straightened out).

Could you please either make sure to keep both up to date, or
alternatively drop it from CRAN?  I'm sure the CRAN master can tell
you how to do this.

Cheers,

/Henrik