Yes adding BiocManager to the suggest field of your DESCRIPTION will likely correct the ERROR
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 bora.u...@mdc-berlin.de <bora.u...@mdc-berlin.de> Sent: Monday, October 30, 2023 7:01 AM To: Herv� Pag�s <hpages.on.git...@gmail.com>; bioc-devel@r-project.org <bioc-devel@r-project.org>; Kasper Daniel Hansen <kasperdanielhan...@gmail.com> Subject: Re: [Bioc-devel] [ext] Re: RCAS build error on Nebbiolo2 - Missing BiocManager Dear Herve & Kasper, Thank you very much for your responses. The checkSeqDb(�hg19�) function calls the BSgenome::available.genomes function which in turn calls �get_data_annotation_contrib_url<https://secure-web.cisco.com/1fvh4WUp6rrult1rI78RZ3xoBehNXKaBnvMRvwcC-pQ83McSrfbOrZ_m2FrP7UmTtEWuiJh8RPmRpvguEjef0aicUatFoq7xtHMczN4OlA5vN8WdKLeK7JJakkoSiDCQcl01EOyNp5IrMKU-Dl8Jv7muVtQEobg_3Ngw71nrLqqh-Dtl9ISJpe07zFK5_JvOoI1ze39ieR2-Y-xAnlArXl-i3ALcWSGCUojrcqL08w48xkU7_MZAv0ymeq2nXyN9V-iNtz7rFECcFxS3D4CC70IprYiexW0VoMLq0zHDoaINQD9JcsyIU8wLS4RdNGvS0/https%3A%2F%2Frdrr.io%2Fbioc%2FBSgenome%2Fsrc%2FR%2Futils.R>�. The method tries to access `BiocManager::repositories` function to find a certain url. So, it basically fails because BiocManager is not seen, not because it is used to install a dependency here. In this case, it would be okay add BiocManager to the suggests field of my package, is that right? Best, Bora From: Herv� Pag�s <hpages.on.git...@gmail.com> Date: Friday, 27. October 2023 at 17:57 To: "Uyar, Bora" <bora.u...@mdc-berlin.de>, "bioc-devel@r-project.org" <bioc-devel@r-project.org> Subject: [ext] Re: [Bioc-devel] RCAS build error on Nebbiolo2 - Missing BiocManager Hi Bora, BiocManager is installed on the machine but 'R CMD check' does not "see" it because you don't have it listed in Suggests. This 'R CMD check' behavior is controlled by the _R_CHECK_SUGGESTS_ONLY_ behavior and is only enabled on our Linux builders for now. However, please note that the code in your examples, vignettes or unit tests should NOT install packages. I don't know what package exactly checkSeqDb('hg19') is trying to install but that is what should be listed in Suggests instead of BiocManager. That way it won't be reinstalled over and over again by 'R CMD check'. Best, H. On 10/27/23 05:56, bora.u...@mdc-berlin.de<mailto:bora.u...@mdc-berlin.de> wrote: Hi Bioc-Devel Team, My package RCAS has been getting build errors on Nebbiolo2. It fails to run the tests/examples/vignettes all due to a missing dependency, which can�t be installed because BiocManager is not available. Here is the build report: https://secure-web.cisco.com/1oc6eAjZ-FE8AObjfGH03qE9a1hOsiCxwHEaWQ-JVoXYs0UcJT25xFT64UwaVhGp5rAqFSt8WYTYvfa-OBhEqJMA5VtX-aGdpBu73H3Sr9H1Eici0Om_Y0Qm9isMcqJEA4iWwvxOnVpkX0_0dPV1PBCJEL9enWks0R6cOW_61R_-np4RpsVWEsfsvT8XIItL5ytDO6mphyIsl7Yo4qBZ2PxWqUVbmtvRx-VGstVKQ1NB9j6RINF91QrgFdolsHWGZQA8dXvGmRJVZlkzpHy1iZZIda8sAk0n6Otz6jSGm4MfME-tlgeMbqFyssvkK_rOj/https%3A%2F%2Fbioconductor.org%2FcheckResults%2Frelease%2Fbioc-LATEST%2FRCAS%2Fnebbiolo2-checksrc.html The relevant error is : Error in get_data_annotation_contrib_url(type) : Install 'BiocManager' from CRAN to get 'BioCann' contrib.url Error: processing vignette 'RCAS.vignette.Rmd' failed with diagnostics: Install 'BiocManager' from CRAN to get 'BioCann' contrib.url The other machines all build it properly. Best, Bora ----------- Dr. Bora Uyar Bioinformatics Scientist Bioinformatics and Omics Data Science Platform Max Delbrueck Center (MDC) for Molecular Medicine The Berlin Institute for Medical Systems Biology Hannoversche Str. 28, 10115 Berlin [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://secure-web.cisco.com/1ys404GvGqDvctdVGqC6rbba7cu4ndBj7rX8GOxBdEWCDj9GJFZJX1r6UXp9wvI3FwqSAJgqs3zJK1_Q5WeTGBnUAoseKncxC9KUmUdgVLnVA--evyOyEOEjUZj_Bae5ef04klmu9Kc3mg6IdwDfyBIFsUaPx2N4-0G92lknbxcmaw5tNm-bVredR-k3q-fdXKE7eIxa2mLHozJbecGCksie0WRbeNalSPrzqTQSq2A44xne7XrjY8eg9M0DlovlfQrqkrpaffTyRwFem5LZDNc3k5xyUjb16j4avDDH_6R_tUyTuKKFUEwRhiAt4mHUH/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel -- Herv� Pag�s Bioconductor Core Team hpages.on.git...@gmail.com<mailto:hpages.on.git...@gmail.com> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1ys404GvGqDvctdVGqC6rbba7cu4ndBj7rX8GOxBdEWCDj9GJFZJX1r6UXp9wvI3FwqSAJgqs3zJK1_Q5WeTGBnUAoseKncxC9KUmUdgVLnVA--evyOyEOEjUZj_Bae5ef04klmu9Kc3mg6IdwDfyBIFsUaPx2N4-0G92lknbxcmaw5tNm-bVredR-k3q-fdXKE7eIxa2mLHozJbecGCksie0WRbeNalSPrzqTQSq2A44xne7XrjY8eg9M0DlovlfQrqkrpaffTyRwFem5LZDNc3k5xyUjb16j4avDDH_6R_tUyTuKKFUEwRhiAt4mHUH/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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