[Bioc-devel] Update existing packages and change name

[Obenchain, Valerie]

Builds run once a day starting at 5pm EST. Commits made before that time will be included in the next day's build report.

Did you commit changes to the Bioconductor git server and not just github? If they made it to the git server you will see them in the logs. Check the logs.

Did you bump the versions?

If all this is 'yes' then report what versions you think should appear on the build report vs what you are seeing.

Valerie


On 03/13/2018 06:39 AM, Sokratis Kariotis wrote:
Hey,

it was a bit smaller before we update the data and I guess it didn't trigger the restriction. I will add it to the data package then. In another matter, I pushed changes (last Friday and yesterday) to the master and upstream for all 4 packages I want to update (pathprint, pathrpintGEOData, pcxn and pcxnData) but I cannot see the changes in the BioC 3.7 (I mean that the new versions havent been checked). Does it take more time or additional steps are required? Thanks!

Cheers,
Sokratis

On 12 March 2018 at 19:16, Obenchain, Valerie <Valerie.Obenchain at roswellpark.org<mailto:Valerie.Obenchain at roswellpark.org>> wrote:
Hi,

There is a max file size restriction of <= 5MB for software packages. This information was missing from our package guidelines so I've just added it.

The built tarball for a software package is restricted to <= 4MB so files over 5 MB aren't a good idea. Why so much data in the software package? Since you have the companion data package the larger files should go there. Ideally the software package will just have enough for man pages and small examples/tests.

Valerie




On 03/12/2018 08:35 AM, Sokratis Kariotis wrote:
Hey Valerie,

I tried to push a new version of pathprint and pathprintGEOData packages (no new files (just updated the existing) and no renaming of packages). pathrintGEOData seem to be fine but when I tried to push pathprint upstream I got an error which stated that one of my files (chipframe.rda, which got a bit more data) is now larger than 5mb and the push hwas aborted. What can I do about this? Thanks in advance.

Regards,
Sokratis

On 21 February 2018 at 20:37, Obenchain, Valerie <Valerie.Obenchain at roswellpark.org<mailto:Valerie.Obenchain at roswellpark.org>> wrote:
Hi Sokratis,

Unfortunately you can't rename a package ... and there is no such thing as a 'sub package'. Maybe you meant sub-package terms of dependencies. If you have new data to add that's independent of what's in pathprintGEOData you can create a new data package.

I'm not sure what you mean by 'considerably more data'. The pathprintGEOData package is currently 22MG:

~ >du -h pathprintGEOData_1.4.0.tar.gz
22M    pathprintGEOData_1.4.0.tar.gz

We don't support git LFS yet in the experimental data repo. If you plan on making the package(s) very large we should consider making a ExperimentHub package where the data can be stored in S3.

Valerie



On 02/21/2018 05:16 AM, Sokratis Kariotis wrote:

Hey all, I am updating 2 of my packages (pathprint & pathprintGEOData) with
considerably more data and a few code updates. I also want to change the
name of the data package to reflect the new content. Can the package name
be changed or do I have to create new sub-packages? Thanks in advance.

Cheers



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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.
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