[Bioc-devel] Package crashes with

Benilton Carvalho beniltoncarvalho at gmail.com
Thu Feb 2 20:01:47 CET 2012

Hey Laurent,

The major issue, IMHO, is the fact that internally ggplot2 has
distinct dependencies conditional on its version. ggplot2 0.8.9
depends on reshape; ggplot2 0.9.0 depends on reshape2. And both
reshape and reshape2 provide different implementations of the same
method (see melt).

If ggplot2 0.9.0 was available for every platform, the changes in
GRENITS (and whatever other package that uses ggplot2) would be
straightforward (but still require some extra work, given how the
format of some outputs from reshape2 changed compared to reshape)...
And it does not seem to me that these are changes that we expect to do
in the middle of a cycle on the stable branch.

One particular issue is the fact the Hadley mentioned that ggplot2
0.9.0 would be resubmitted to CRAN only in March ( http://goo.gl/p5rbq
)... which makes this slightly harder to handle.

Maybe we'd need to have one exception and simply force to have ggplot2
0.8.9 on the stable branch? Or just solve the issue that impedes
ggplot2 0.9.0 to be built on every platform and deal with the fact
that there would be major (internal) changes on the BioC release


On 2 February 2012 18:25, Laurent Gatto <laurent.gatto at gmail.com> wrote:
> Dear Edward,
> I believe the error is the result of ggplot2 v 0.8.9 depending on
> reshape while ggplot2 v 0.9.0 now imports reshape2. You now need to
> load reshape/reshape2 explicitly in your vignette prior to calling
> melt. Note that this change will have to be committed to devel and
> RELEASE, as ggplot2 has been updated on both branches.
> Hope this helps,
> Laurent
> On 2 February 2012 14:56, Edward Morrissey
> <edward.morrissey at cancer.org.uk> wrote:
>> Hi,
>> I am the maintainer of GRENITS package. It has recently started to give
>> build errors due to a function it uses from
>> the package ggplot2. I've updated ggplot2 to the latest cran version (0.8.9)
>> and it's dependencies but cannot replicate the errors.
>> However, I found a newer version of ggplot2 (0.9.0) on crantastic that
>> relies on the new package reshape2 (previously it used reshape).
>> Could the problem be that ggplot2 was updated to the latest version (0.9.0),
>> but reshape2 was not installed? How can I check the versions
>> of the packages used for the build process?
>> Thanks,
>> Edward
>> _______________________________________________
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