[Bioc-devel] Package crashes with

[Dan Tenenbaum]

On Fri, Feb 3, 2012 at 9:42 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> Hi all,
>
> On Fri, Feb 3, 2012 at 6:30 AM, 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.
>>
>
> It appears that ggplot2 0.9.0 was available through CRAN and then
> withdrawn to 0.8.9 (except on Mac, where 0.9.0 is still available).
> The Bioconductor build system installs from CRAN and tries to load the
> newest packages available. I removed ggplot 0.9.0 from the build
> machines which will trigger the installation of 0.8.9 in the next
> build cycle. I will ask Hadley about why 0.9.0 is available for Mac
> only.
>

Hadley has asked CRAN to pull ggplot2 0.9.0 for Mac and it looks like
it indeed has reverted to 0.8.9 on the CRAN master. When this
propagates to our CRAN mirror, I'll make sure we have 0.8.9 on our Mac
build machine so all are consistent.

Hadley also asked me for the email addresses of all BioC maintainers
who depend on ggplot2. I imagine he will be in touch with you with
information about how to make the transition when the time comes.

Thanks,
Dan


> Thanks,
> Dan
>
>
>> 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 ]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel