[Bioc-devel] Dependency update propagation (rcdk on morelia)

[Hervé Pagès]

Hi Nan, Zach, Val,

On 12/05/2016 01:45 PM, Obenchain, Valerie wrote:
> Hi,
>
> We need to make several updates to the mac machines. These are the last
> 2 builders that still need to move from the Hutch to RPCI. Because they
> are still at the Hutch, access to them is limited. We will get to these
> updates as soon as we can.

Yes, we'll do this soon.

However please note that rcdk also fails to pass check on the Mac
builder on CRAN because the builder doesn't have Java >= 7 either:

 
https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks/rcdk-00check.html

As a consequence the version of the Mac binary for rcdk is lagging
behind the source package:

   http://cran.fhcrc.org/web/packages/rcdk/index.html

   Source package version: 3.3.8
   Mac binary version: 3.3.2

Most of the BioC users that are on Mac are not set to install packages
from source and need to be able to install binary packages.

So even if we update Java on our Mac builders, most Mac users still
won't be able to install the latest rcdk and Rcpi.

Cheers,
H.

>
> Valerie
>
>
>
> On 12/05/2016 01:27 PM, Dan Tenenbaum wrote:
>> Actually it looks like the version of java installed on morelia is 1.6. So it appears that 1.7 (or higher) needs to be installed.
>>
>> Dan
>>
>>
>> ----- Original Message -----
>>> From: "Zach Charlop-Powers" <zach.charlop.powers at gmail.com>
>>> To: "Nan Xiao" <road2stat at gmail.com>
>>> Cc: "bioc-devel" <bioc-devel at r-project.org>
>>> Sent: Monday, December 5, 2016 1:02:52 PM
>>> Subject: Re: [Bioc-devel] Dependency update propagation (rcdk on morelia)
>>> Hi Nan,
>>>
>>> rCDK 3.3.6 requires Java8 and will throw error if the Java environment is
>>> incorrect.  BioC Build only has Java7 hence the error. The new version of
>>> rCDK requires Java7. Once rcdk 3.3.8 makes it onto the BioC builds (its on
>>> CRAN), these errors should clear up.  Please keep me posted if they don't.
>>>
>>> zach cp
>>>
>>> On Mon, Dec 5, 2016 at 3:43 PM, Nan Xiao <road2stat at gmail.com> wrote:
>>>
>>>> Hey guys,
>>>>
>>>> - it seems this problem is also affecting the other two Bioc packages
>>>> depending on rcdk, i.e. RMassBank and rcellminer (release + devel). Any
>>>> ideas why?
>>>>
>>>> Thanks,
>>>> -Nan
>>>>
>>>> On Fri, Dec 2, 2016 at 2:29 PM, Nan Xiao <road2stat at gmail.com> wrote:
>>>>
>>>>> Hi Bioc,
>>>>>
>>>>> - the Rcpi package depends on rcdk, and the rcdk package was updated last
>>>>> week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which
>>>>> removed the Java > 1.8 requirement (previously discussed in
>>>>> https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ).
>>>>>
>>>>> I've updated the Rcpi package and specified the rcdk version to be >=
>>>>> 3.3.8, while the most recent Mac build gives the error: (
>>>>> http://bioconductor.org/checkResults/release/bioc-LATEST/
>>>>> Rcpi/morelia-buildsrc.html )
>>>>>
>>>>> namespace 'rcdk' 3.3.6 is being loaded, but >= 3.3.8 is required.
>>>>>
>>>>> So it seems morelia is still using rcdk 3.3.6, while this >= 3.3.8
>>>>> version requirement is fulfilled by Linux and Windows builds (if I
>>>>> understand correctly).
>>>>>
>>>>> Is there anything I could do to solve this issue?
>>>>>
>>>>> Thanks a lot,
>>>>> -Nan
>>>>>
>>>>> --
>>>>> http://nanx.me
>>>>>
>>>>
>>>>
>>>> --
>>>> http://nanx.me
>>>>
>>> 	[[alternative HTML version deleted]]
>>>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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