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

[Kern, Lori]

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

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