[Bioc-devel] import questions

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Sun Dec 4 19:35:20 CET 2011

For the last while minfi has failed to build in devel.  It fails with
a rather arcane error message

* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading

by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt

Error in generics[[i]] : subscript out of bounds
ERROR: lazy loading failed for package ‘minfi’
* removing ‘/tmp/RtmpfDVi1h/Rinst546d4609/minfi’

For a while I thought this was related to BiocGenerics, but I have now
tracked it down.  This problem occurs if I have
  importMethodsFrom(Biobase, show)
in my NAMESPACE file.  It does not appear if I have

This is rather weird.  And I don't understand why show is different
from say initialize.  I don't see how either Biobase nor minfi treats
show in any way different from initialize.

Some (irrelevant) background: If I use import(Biobase) it conflicts
(resulting in a warning message) with matrixStats, so I have attempted
to work around this by selectively importing Biobase.

Anyone who has any idea what is different between show and initialize here?


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