Thank you for the help! I'll try to fix in time. Best, Evan
On Wed, Apr 19, 2023 at 7:56 AM Kern, Lori <lori.sheph...@roswellpark.org> wrote: > We encourage developers to fix any warnings but warnings will not prevent > a package from being included in the release. > > Cheers, > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Evan Biederstedt <evan.biederst...@gmail.com> > *Sent:* Tuesday, April 18, 2023 9:39 PM > *To:* Kern, Lori <lori.sheph...@roswellpark.org> > *Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org> > *Subject:* Re: [Bioc-devel] taking over package, fixing build error > > 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 > <https://secure-web.cisco.com/1qrzIvSRXS_i2iJlFStzE2GqXrNhrN-b7OWOCQlOQ5VTKflTf4vzB4YU3J-ypIDbhhwTTEGnsBnDcsRg-eYLdkKkWySbZdkce8jdENiayQy-dbNyq6k6xqUjCWW2jAI0-BI21xabej5IA8QtARjwgyUIybMI0O2ayQMdV19sYLHjtSLCZ_W4BAsBCvkcU5u36EHTZgYtZjubEwSJi82dLU3OJWaCq2LduWDNdnneew9mHf67kmWJII5HAzhclUSZfWxVg1-mv4IkuwngW81Uc9-7fqmEb54b92Or3H-5fIl2Q2lwSnvyzcDbjwc76G6kE/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.17%2Fbioc%2Fhtml%2Fscde.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.sheph...@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/ > <https://secure-web.cisco.com/11v5lVewxhls0q9aBHQOIdTMCr4n0o_01ZLllh9JHwIZ4Ha__iq4i7n8qgnbi3QWKElWp1fvEOmjYUCan8Mqs2OwddahRAXm9MguLLBqA8nRbq5VAuK4_h0ReEGazZdTAQSf6TN6xVmM1KG3y7qmHXjyEVh4wUdo1eOpsI7sw-Do7f8-lHOuFkoXNdq71RR2RvVDgyD-vkwTgSAuHssoB6x29jo3NIxwP9K80LLFVCxKPNvBduS5jGotbNGAQm_ZycgCOgo4PGSozU6jd6wo2xQyHcWxJy7jgFIVqKWipZ86D1SPbOsqa3ueJRCgoIkMB/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.17%2Fbioc-mac-arm64-LATEST%2F> > > The report for linux, mac, and windows is found here: > > https://bioconductor.org/checkResults/3.17/bioc-LATEST/long-report.html > <https://secure-web.cisco.com/1jTMMBM07mpPbM14cz9Iz9EwVZzWb94QZ_r8z6RZaZZkio_sdjBEQVz-lUauOAVM8r8zivUso6FxPvFdIDXx9vJ_cJIXTnqxFh6BtPFkEYs3CXTZ4-VAZHRHnDOBEWqb4xj_6r4xSb0tJhElf59nt89aiebsW1QwR-xncC5CZUh7r1DKFoOuidKA-g14Y0flPUqVmPk-N8NkxNoOS7dPG8nhlyG2KxVto5alvmL4PjFdkozKmZ3PNvahRQBk61drSvUGhJobDwjmALN7VLq48uVSkqZcdvYP87qMczXMLsw8U4M1iqqNQvOTcptSe0GmL/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.17%2Fbioc-LATEST%2Flong-report.html> > > And the main check results page shows the schedule for builds. > > https://bioconductor.org/checkResults/ > <https://secure-web.cisco.com/1kwPNJ0J_odRmRnJTZZZ7vfBiehy8cIH80lL7rItYDCZoIZsoP26pD19Lvh3FqQ6rTMPyA_6FZzytkhdgA4ffNYDVUmFzV2gywOvFrlMpjCfqDV__emnS079FNQ_zwjXM_e2VPiQTGsjnhp_oP7UtwFC-Nk8fYSoOVHQ9kRL-0LrtSX9eaHt1hp8rOj4ojOBrxAbOCMFB6JiC0aBr9BzQqpz3bOh7SmasKh_1Y3VOPeSkbnraiJsaFWDvgoXCsuGGcG69RgG2knvZ4PIG2K7_ZTvczFZGELIZUxxIudVA0eqj6ZVf70hlNXRKiTpMRNDC/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F> > > 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-boun...@r-project.org> on behalf of Evan > Biederstedt <evan.biederst...@gmail.com> > *Sent:* Saturday, April 15, 2023 2:41 PM > *To:* bioc-devel@r-project.org <bioc-devel@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 g...@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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > > https://secure-web.cisco.com/1vw9O3UyR1Y940C0zKjB-tiK-baXutUvpqC50dO_ZMW9jGyZh3fM7NOTLB8S5uzYEIqLANYLZQHw5nF2BdwurussfEc3zsmUtjxWXaHuYqBJlp1LJ53f6M7z4QYxBaz_JyKYK64KWj06lg-ncs3yrpzn2ABDnHIOQd-ZdBtcuEPfkcs6PIvscw0XPlJezUO-UaObluDYVZPngy7sGFNtK2WK4NBJp0jT0jVuRcp7L1wq83lJI8TK4qqLywON-VsdKJKOxQKQLr3i5JA1s5PpIugD8FrHLc478bmpvjPQyaBBlvchquCx7wiJTQeTA9HV1/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > This email message may contain legally privileged and/or confidential > information. 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