[Bioc-devel] [ext] Re: RCAS build error on Nebbiolo2 - Missing BiocManager

[Kern, Lori]

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-bounces using r-project.org> on behalf of Bora.Uyar using mdc-berlin.de <Bora.Uyar using mdc-berlin.de>
Sent: Monday, October 30, 2023 7:01 AM
To: Herv� Pag�s <hpages.on.github using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>; Kasper Daniel Hansen <kasperdanielhansen using 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.github using gmail.com>
Date: Friday, 27. October 2023 at 17:57
To: "Uyar, Bora" <Bora.Uyar using mdc-berlin.de>, "bioc-devel using r-project.org" <bioc-devel using 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.Uyar using mdc-berlin.de<mailto:Bora.Uyar using 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







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--

Herv� Pag�s



Bioconductor Core Team

hpages.on.github using gmail.com<mailto:hpages.on.github using gmail.com>

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