[Bioc-devel] Interpreting BiocCheck output

[Martin Morgan]

Just my two cents, but I don’t think using `globalVariables()` is a good idea in a package – it’s too easy to say that R should ignore a variable that it should not.

In the context of dplyr, the alternative is to `importFrom dplyr .data` or to use ‘standard’ evaluation, depending on circumstance


> mtcars |> as_tibble() |> filter(.data$mpg > 30)  # .data is imported, so known…
# A tibble: 4 × 11
    mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb
  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1  32.4     4  78.7    66  4.08  2.2   19.5     1     1     4     1
2  30.4     4  75.7    52  4.93  1.62  18.5     1     1     4     2
3  33.9     4  71.1    65  4.22  1.84  19.9     1     1     4     1
4  30.4     4  95.1   113  3.77  1.51  16.9     1     1     5     2
> mtcars |> select("mpg", "cyl") |> head(3)  # `”mpg”` and `”cyl”` are character vectors, not symbols…
               mpg cyl
Mazda RX4     21.0   6
Mazda RX4 Wag 21.0   6
Datsun 710    22.8   4

Martin

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Marcel Ramos <marcel.ramosperez using roswellpark.org>
Date: Friday, October 7, 2022 at 3:07 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Interpreting BiocCheck output
Hi Giulia,

Thanks for sharing.
I took a look at https://github.com/calabrialab/ISAnalytics and I'm glad
you resolved the issue.

Just a reminder, you can also use `utils::globalVariables('.')` in your
package for functions
that use `'.'` (and other symbols) as a variable, e.g. in `purrr::pmap`.

Best regards,

Marcel


On 10/6/22 4:34 AM, Giulia Pais wrote:
>
> 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
> >
> >        [[alternative HTML version deleted]]
> >
> >
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