[Bioc-devel] EXTERNAL: Interpreting BiocCheck output

[Giulia Pais]

Hi, thanks for the reply. I managed to fix the first error as it was a minor issue in the code, while for the second one I don’t have a solution since the problem appears only locally and not on Biconductor after the build.

Just for reference the package is ISAnalytics and the BiocCheck version is the latest one.

Thanks again,
Giulia

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Marcel Ramos <marcel.ramosperez using roswellpark.org>
Date: Wednesday, 2022October5 at 23:48
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] EXTERNAL: Interpreting BiocCheck output
Hi Giulia,

Are you using a recent version of BiocCheck?

If so, check the bottom of the BiocCheck::BiocCheck():

---
See the <packageName>.BiocCheck folder and run
     browseVignettes(package = 'BiocCheck')
for details.
---

Can you provide more details, e.g., the repository of the package?

Thanks.

Best regards,

Marcel

On 10/4/22 4:44 AM, Giulia Pais wrote:
> Hello,
> I�m having some issues in interpreting BiocCheck outputs, maybe someone can tell me how to fix the issues.
>
> I�ve got 2 main issues that cause the check to fail after normal CRAN check has passed:
>
>    1.  I get this error message
>
> * Checking if other packages can import this one...
>
>      * ERROR: Packages providing 2 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing
>
>        this package may fail.
>
>
>
> However it is nowhere mentioned which packages they are and where those objects are instantiated so I have no clue how to solve this one
>
>    1.  Since previous version of the package, which built and passed checks without issues, I�ve been using a custom *.Rmd file placed in inst/rmd in the vignette to recycle the same chunk of code and optimizing time in phase of update (I update info only once instead of 4 times). Even if the package passes CRAN checks, BiocCheck errors telling me it can�t find this Rmd file and therefore can�t evaluate the chunk where it is mentioned. Any suggestion on this?
>
> Thanks in advance
> Giulia
>
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>
>
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