Hi guys,
On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
Hi Sokratis,
I added the .BBSoptions file to pcxn when it should have been added to
pcxnData. The .BBSoptions file should be put in the package that 'Suggests'
(not 'Depends') on the other. In this case it's pcxnData that needs the
.BBSoptions. Sorry for the mix up, this has been fixed.
The data package should install with today's builds and be clean on the
Saturday report. The software package should then install with the Saturday
builds and be clean on the Sunday report.
This is what should happen:
- pcxnData should install with today's data-exp builds (they
started this morning) but vignette will still fail (pcxn still
missing)
- pcxn won't install (will be back to NotNeeded) but should pass
build/check and propagate on Saturday afternoon
- on Sunday morning, the data exp builds will find pcxn **on line**
(because now it propagated) so will be able to install it so
vignette will finally build and the package will propagate
Thanks for taking care of this,
H.
Valerie
On 10/26/2017 04:26 AM, Shepherd, Lori wrote:
We have already taken care of this on our end and you shouldn't need to do
anything else. As always changes reflected may take a few days to reflect in
the build reports.
The solution is to add a .BBSoptions file with ForceInstall: TRUE to the
software package. Since there is a circular dependency this will force install
the software package even though there will be ERRORs because of the missing
data package. On the next build of the data packages, the data package will
then successfully build finding the software package. Then following, the
software package will also build finding the data package.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel
<bioc-devel-boun...@r-project.org><mailto:bioc-devel-boun...@r-project.org> on behalf of
Sokratis Kariotis <s.kario...@sheffield.ac.uk><mailto:s.kario...@sheffield.ac.uk>
Sent: Thursday, October 26, 2017 4:02:53 AM
To: bioc-devel
Subject: [Bioc-devel] Accepted packages can't find each other and fail build
Hey all,
I created 2 packages that got accepted (pcxn and pcxnData) where pcxn
depends on the data coming from pcxnData. However, in the vignettes of
pcxnData I am using library(pcxn) to demonstrate what can you do with the
data. As a result both packages fail building in BioC 3.6 as they can't
find each other. In a previous pair of packages I am maintaining (pathprint
and pathprintGEOData) I could use the first library in the data package
vignette and building was fine. Is it necessary to remove library(pcxn)
from pcxnData to get them build? Thanks in advance!
Cheers
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
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