[Bioc-devel] New build report

[Alina Selega]

Hi,

First of all, thank you very much for pointing me to the resources -- and
apologies for my confusion!

I have now applied changes correctly to both RELEASE_3_8 and devel branches
in order to fix the warnings on tokay2 arising from missing links when
calling external functions. By looking at the build report for the devel
branch, I see that I dealt with one warning, but the other one persists ("file
link 'stri_locate_all' in package 'stringi' does not exist and so has been
treated as a topic"). I cannot reproduce this warning when running
devtools::check() in the latest RStudio on a Windows 10 machine.

I also noticed that the latest build report from RELEASE_3_8 is not
including the Windows server so I don't know if the warning shows up there
too. Do you have any advice?

Thanks,
Alina

On Fri, 12 Apr 2019 at 12:29, Alina Selega <alina.selega using gmail.com> wrote:

> Okay, thank you very much!
>
> On Fri, 12 Apr 2019 at 12:25, Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> wrote:
>
>> That is not correct. The webhook was only for the package submission
>> process.
>>
>> See the link provided on linking to Bioconductor.
>>
>> Other helpful github links  can be found here:
>> http://bioconductor.org/developers/how-to/git/
>>
>>
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>> ------------------------------
>> *From:* Alina Selega <alina.selega using gmail.com>
>> *Sent:* Friday, April 12, 2019 12:22:40 PM
>> *To:* Shepherd, Lori
>> *Cc:* bioc-devel
>> *Subject:* Re: [Bioc-devel] New build report
>>
>> Thank you for the instructions!
>>
>> Can I just clarify -- I was pushing changes to my Github repository that
>> has a webhook set up (as per instructions from when I first submitted the
>> package to Bioconductor). I thought that pushes to master branch with
>> version bump should trigger package builds. Am I wrong about this?
>>
>> Thanks,
>> Alina
>>
>> On Fri, 12 Apr 2019 at 12:15, Shepherd, Lori <
>> Lori.Shepherd using roswellpark.org> wrote:
>>
>> We are not seeing the changes pushed to the git.bioconductor server.  I
>> am assuming you are referring to the RELEASE_3_8 branch since you are
>> referencing 1.6.1.
>>
>>
>> Have set up the remote upstream to point to Bioconductor,
>>
>> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>>
>>
>> On your repository you can check your remotes with
>> git remote -v
>>
>> It should include something like the following:
>> upstream git using git.bioconductor.org:packages/BUMHMM.git (fetch)
>> upstream git using git.bioconductor.org:packages/BUMHMM.git (push)
>>
>> Make sure you pushed to the upstream remote:
>>
>>
>>
>> http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
>>
>> and that you are working on the RELEASE_3_8 branch
>>
>> git fetch --all
>>
>> git checkout RELEASE_3_8  (or git checkout upstream RELEASE_3_8)
>>
>> # make your changes
>>
>> # commit your changes
>>
>> # push the changes to Bioconductor with the following:
>>
>> git push upstream RELEASE_3_8
>>
>>
>>
>>
>> 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 using r-project.org> on behalf of Alina
>> Selega <alina.selega using gmail.com>
>> *Sent:* Friday, April 12, 2019 12:04:03 PM
>> *To:* bioc-devel
>> *Subject:* Re: [Bioc-devel] New build report
>>
>> Hi,
>>
>> Sorry, I think I must have done something wrong as the build report is not
>> showing the updates to my package from 2 days ago. Could you please help
>> me
>> with this? I thought I updated the version of BUMHMM correctly (from 1.6.1
>> to 1.6.2 and 1.6.3) but it is not been picked up?
>>
>> Thanks,
>> Alina
>>
>> On Thu, 11 Apr 2019 at 12:47, Alina Selega <alina.selega using gmail.com>
>> wrote:
>>
>> > Hi,
>> >
>> > I have made some minor updates to my package (BUMHMM) yesterday to fix
>> the
>> > warnings arising on the Windows server and pushed the changes with a
>> > version bump from its current version 1.6.1. (actually, two bumps.)
>> >
>> > I don't see any changes in today's build report; has the build happened
>> > yet?
>> >
>> > Thanks,
>> > Alina
>> >
>>
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>>
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