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.sel...@gmail.com> wrote: > >> Okay, thank you very much! >> >> On Fri, 12 Apr 2019 at 12:25, Shepherd, Lori < >> lori.sheph...@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.sel...@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.sheph...@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 g...@git.bioconductor.org:packages/BUMHMM.git (fetch) >>> upstream g...@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-boun...@r-project.org> on behalf of Alina >>> Selega <alina.sel...@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.sel...@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]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=osHeAg_D9QHiH847n5dDe9w5QRirbiorSXmEw3-8KGI&s=fvsfUASkAYSrrwKTz8GcAHfKIQOjOg96gxxv26C77ns&e= >>> >>> 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. 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Thank you. >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=osHeAg_D9QHiH847n5dDe9w5QRirbiorSXmEw3-8KGI&s=fvsfUASkAYSrrwKTz8GcAHfKIQOjOg96gxxv26C77ns&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel