[Bioc-devel] taking over package, fixing build error

[Evan Biederstedt]

Hi Lori

Thank you so much for helping clarify this. I'm still learning the ropes.

Ok, I could wait for the builds.

So this is the development version of scde with fixes.
https://bioconductor.org/packages/3.17/bioc/html/scde.html
Please see the screenshot attached.

Very naïve question: Is the package now fixed and ready for 3.17? It looks
like there's no problems except with "warnings" for "check".

In the CRAN universe, this is a failure and it would be removed/not
accepted. Is it ok here for the upcoming release?

Thank you for the help!

Best, Evan



On Mon, Apr 17, 2023 at 7:56 AM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> Note the link you provided is only for mac arm 64 builds
>
> https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/
>
> The report for linux, mac, and windows is found here:
>
> https://bioconductor.org/checkResults/3.17/bioc-LATEST/long-report.html
>
> And the main check results page shows the schedule for builds.
>
> https://bioconductor.org/checkResults/
>
> As far as testing for if it works, most just wait.  Trying a run with the
> correct version of R and Bioconductor and ensuring all packages are
> valid/up-to-date with BiocManager::valid and BiocManager::install can help
> too.  There are Bioconductor dockers available that try to mimic the build
> system environment that can be beneficial too. Hope that helps a little.
>
> Cheers,
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Evan
> Biederstedt <evan.biederstedt using gmail.com>
> *Sent:* Saturday, April 15, 2023 2:41 PM
> *To:* bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject:* [Bioc-devel] taking over package, fixing build error
>
> Hi BioConductor devel community
>
> (Apologies if these are obvious questions; I haven't quite grokked the
> answers from the documentation.)
>
> I'm someone who has submitted in the past to CRAN, but this is my first
> rodeo with Bioconductor. Please be patient with me :)
>
> I'm taking over as a maintainer for this package:
>
> https://secure-web.cisco.com/17YjCGhDwIrU1ClZrmjvB3lSR7k0_8S5Fd3mMrD2C2Md_g8Z7MqEoWAd9XzBKkNcHgRJ2ggE32elkpbkNFbfZxNEpJUZrTv17t0sJ8t_ZW2PPwNUJXBBpnbGEsih8h4qntwMAvCv_BaZnA11MU_khCiVJubDi-nh7-M-MwCHEdRavahr7I2fwCFFAk_TksrIaR246nfDYOArvyF9Jirgbj__dycJ3ej0vlMZlUznY2x8z4RUZRo3HgfP-Td6_IJyPSYganZjwyIAiaY10l1Rnw1PRXwBGX5FGkidS7UZl00rxHPplf2meEM1L4dxyqN23/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Fscde.html
>
> There was an issue with the compilation of scde (related to C++17 and
> deprecated C++ function).
>
> https://secure-web.cisco.com/1pjgPdAGYbFi9-qIcpXg4ITO0Ra6S3p38gG2qj_wtmRTNhuzGhzIIC-m-UiVaZp3W0USgbZF-gQcK2KTgoGZtbeROAPokOogr76J3hzlaxsVmnpgJynOexIpyTOFfssnWyU6sl2_AnQlXe4TT0rUSzHJrNBWv5dgtUjOi33fe0Fw9dam8Sl5_nxRm7fbIm_8Jz7WE19HqKsjJ9w8irjOdFmRf7RQtXAgkadurHx1pIqbQnCdcrWdSK8Tf5cADC5lPjN_ZgO_9pW_sf-aC3ErYX9I9qvfxQ74mHKHVhthRLtchbXgtFnPQFd4PQYtUjEQT/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.17%2Fbioc-mac-arm64-LATEST%2Fscde%2Fkjohnson2-checksrc.html
>
> I think I've fixed this. So I pushed changes on the `devel` branch in the
> repo from```git clone git using git.bioconductor.org:packages/scde```, following
> the instructions here:
>
> https://secure-web.cisco.com/1hvMPwUdNJsGcO7mY8kqma_3evCgzLQTlFQgCBvpjAKgiDntWPRPz7XPewPqQ7uG9UI1X1gmLR0vXxP6zrlllIr29HbUFdDgBoxcN3A1lqMFRB5VskO7g7QKM5jbBrR2zOqtNWcjSe8B58yjn7w1989sb1_sK-qr9VcgQrS2qD7Vxs95nn8oXMTSSy6qBrupvx9zWjP1p2xKjTrHW0StnV2QL5jrFOLDn0R7zt-htw5F9i_fxfw058WUdE9krT4N9DZ_wq-oNYS7D0unHrSt3oBrni7LY_Tvt_HTkhl23fhciYt_7ivtsYs927kpOI5Ni/https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-version-control.html
>
> My question is, how do BioConductor developers normally check that this
> works? My understanding is that one waits for 24 hours for the packages to
> be re-built, and then developers check the URL here:
>
> https://secure-web.cisco.com/1pjgPdAGYbFi9-qIcpXg4ITO0Ra6S3p38gG2qj_wtmRTNhuzGhzIIC-m-UiVaZp3W0USgbZF-gQcK2KTgoGZtbeROAPokOogr76J3hzlaxsVmnpgJynOexIpyTOFfssnWyU6sl2_AnQlXe4TT0rUSzHJrNBWv5dgtUjOi33fe0Fw9dam8Sl5_nxRm7fbIm_8Jz7WE19HqKsjJ9w8irjOdFmRf7RQtXAgkadurHx1pIqbQnCdcrWdSK8Tf5cADC5lPjN_ZgO_9pW_sf-aC3ErYX9I9qvfxQ74mHKHVhthRLtchbXgtFnPQFd4PQYtUjEQT/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.17%2Fbioc-mac-arm64-LATEST%2Fscde%2Fkjohnson2-checksrc.html
>
> Is there any other way to double check that the commits fix the issue?
> “devtools::check_max_release()” but this often struggles with bioconductor
> packages
>
> Thank you for the help!
> Best, Evan
>
>         [[alternative HTML version deleted]]
>
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