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

[Hervé Pagès]

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 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://bioconductor.org/checkResults/release/bioc-LATEST/RCAS/nebbiolo2-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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>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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