[Bioc-devel] New build report

Mon Apr 15 18:28:25 CEST 2019

Hi Alina,

For some unknown reason tokay1 stopped building in the middle of the 
night so we have no results for Windows on the RELEASE_3_8 build report 
today.

The cause of tokay1's failure is under investigation.

Sorry for the inconvenience,

H.

On 4/15/19 09:23, Alina Selega wrote:
> 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:
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=osHeAg_D9QHiH847n5dDe9w5QRirbiorSXmEw3-8KGI&s=tksi58erFDulZ5od2guQYCrpld161vufCjCcO02r6O8&e=
>>>
>>>
>>>
>>>
>>>
>>> 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,
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=osHeAg_D9QHiH847n5dDe9w5QRirbiorSXmEw3-8KGI&s=2QY95FrrQ_3v7dil1i0P_CA_1ZfeUy7jgtQ7eXIYoJ8&e=
>>>
>>>
>>> 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:
>>>
>>>
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_bug-2Dfix-2Din-2Drelease-2Dand-2Ddevel_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=osHeAg_D9QHiH847n5dDe9w5QRirbiorSXmEw3-8KGI&s=Z4JwI6k7XrrqMORAAa-r_g82QIog2TltWBjbyNAzUD8&e=
>>>
>>> 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
>>>>
>>>          [[alternative HTML version deleted]]
>>>
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> 	[[alternative HTML version deleted]]
>
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-- 
Hervé Pagès

Program in Computational Biology
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