[Bioc-devel] Package crashes with

[Benilton Carvalho]

The issues you're observing are likely associated to the fact that CRAN provides
0.8.9 for Linux and Windows... but 0.9.0 for Mac. b

On 3 February 2012 14:30, Laurent Gatto <laurent.gatto at gmail.com> wrote:
> Dear Benilton,
>
> On 2 February 2012 19:01, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
>> 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).
>
> Definitely, that does have broader implications. Thank you for pointing it out.
>
>> 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
>> branch...
>
> I was surprised that 0.9.0 was installed on the stable branch, as it
> is not yet available on CRAN. Not sure what the best approach is,
> though, as maintainers have or are on their way to make the necessary
> changes in devel and release.
> More confusing, to me at least, is that devel and release packages are
> build/checked with ggplot2 0.9.0 but biocLite installs 0.8.9.
>
> Best wishes,
>
> Laurent
>
>
>> b
>>
>> 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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> [ Laurent Gatto | slashhome.be ]