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.pow...@gmail.com>
To: "Nan Xiao" <road2s...@gmail.com>
Cc: "bioc-devel" <bioc-devel@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 <road2s...@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 <road2s...@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
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