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

[Nan Xiao]

Hi Zach and Dan,

- thanks a lot for the information, that made things much clearer.

>From the build error message, it seems rcdk 3.3.8 only "partially" made to
the BioC builds, which means 3.3.8 is available on Linux and Windows, but
not Mac (still 3.3.6). Maybe I'll just wait for the Java update (and hope
that will propagate the latest rcdk to Mac).

Best,
-Nan

On Mon, Dec 5, 2016 at 4:26 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
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]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
http://nanx.me

	[[alternative HTML version deleted]]