[Bioc-devel] Accepted packages can't find each other and fail build
It should be the same and you should be able to see the RELEASE_3_6 branch git fetch --all git branch -a Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Sokratis Kariotis <s.kariotis at sheffield.ac.uk>
Sent: Tuesday, October 31, 2017 11:20:39 AM
To: Shepherd, Lori
Cc: Herv? Pag?s; Obenchain, Valerie; bioc-devel
Subject: Re: [Bioc-devel] Accepted packages can't find each other and fail build
Sent: Tuesday, October 31, 2017 11:20:39 AM
To: Shepherd, Lori
Cc: Herv? Pag?s; Obenchain, Valerie; bioc-devel
Subject: Re: [Bioc-devel] Accepted packages can't find each other and fail build
Does the same hold for the pcxnData package? I can't see the RELEASE_3_6 as in pcxn.
-Sokratis
On 31 October 2017 at 11:38, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:
The latest version bump change you made to 0.99.27 was yesterday Oct 30 right before we said to stop committing so we could make the release branch. That change did make it into both the RELEASE_3_6 and the master branch and should appear in the next build report for both versions.
Note: It can take 12-24 hours to see version bumps and changes on the build report. The daily builders runs once per day to build all the packages; while a version bump is absolutely required, it is not built instantaneously on a version bump.
Please be sure to pull from upstream before making further changes as we have bumped the versions in both the release and devel versions of packages for the release.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Sokratis Kariotis <s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>>
Sent: Tuesday, October 31, 2017 5:21:21 AM
To: Herv? Pag?s
Cc: Obenchain, Valerie; Shepherd, Lori; bioc-devel
Subject: Re: [Bioc-devel] Accepted packages can't find each other and fail build
Hi all,
There was an error in the pcxn package (and pcxnData as a resut of not finding pcxn since it didnt build) which I fixed yesterday morning, but it doesnt seem to accept my changes as the version in the build report is not the last one I created but the erroneous one (2 days ago). I checked the upstream of my package and it has my latest changes.
Regards,
Sokratis
On 27 October 2017 at 16:57, Herv? Pag?s <hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote:
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-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>><mailto:bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>> on behalf of Sokratis Kariotis <s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>><mailto:s.kariotis at sheffield.ac.uk<mailto:s.kariotis at 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<https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ&entry=gmail&source=g>
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--
Herv? Pag?s
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N<https://maps.google.com/?q=1100+Fairview+Ave.+N&entry=gmail&source=g>, M1-B514
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Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ<https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ&entry=gmail&source=g>
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--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.