[Bioc-devel] Interpreting BiocCheck output

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Oct 11 13:56:23 CEST 2022 

If you are running locally,  there is also a <package>.BiocCheck folder that gets created with a log that has the more specific information as well.

Cheers,


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 Sergio Oller <sergioller using gmail.com>
Sent: Saturday, October 8, 2022 4:38 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Interpreting BiocCheck output

Hi Giulia, hi all

I often run BiocCheck::BiocCheck() on my packages and end up with errors,
warnings and notes that have not printed specific enough messages, just as
you did.

When that happens, on the same R terminal, I use:

BiocCheck::.BiocCheck$error
BiocCheck::.BiocCheck$warning
BiocCheck::.BiocCheck$note

(please note the leading dot after the double colon)

Those three lists include more specific details. Often even the file names
and line numbers where the error occurred (In my experience I've found line
numbers to not be always perfectly accurate, but it's a good enough
approximation).

There may be a better way to get that information through some BiocCheck
log or other reporting facility, but that's convenient enough for me. I
hope this helps you.

Best
Sergio


El dv., 7 d’oct. 2022, 21:49, Henrik Bengtsson <henrik.bengtsson using gmail.com>
va escriure:

> I'm throwing in another 1 cent.
>
> I agree that utils::globalVariables() is risky; since it goes in the
> root of the package code, it applies to *all* functions in the
> package, which is a bit too broad of a stroke for my taste.  The way I
> deal with false globals from non-standard evaluation (NSE), is to
> declare them a as dummy variables local to the function.  In this pl
> case, I would use:
>
> myfcn <- function() {
>   ## To please R CMD check
>   mpg <- cyl <- NULL
>
>   mtcars |> select(mpg, cyl) |> head(3)
> }
>
>
> ADVANCED:
>
> To avoid those dummy assignments from taking place in every call, one
> can also do:
>
> myfcn <- local({
>   ## To please R CMD check
>   mpg <- cyl <- NULL
>
>   function() {
>     mtcars |> select(mpg, cyl) |> head(3)
>   }
> })
>
> which is also a bit cleaner, because it keeps the original function body
> as-is.
>
>
> REALLY ADVANCED:
> If you want to be fancy, you can even protect against mistakes by using:
>
> myfcn <- local({
>   ## To please R CMD check
>   mpg <- cyl <- NULL
>
>   ## Prevent developer mistakes
>   lapply(names(environment()), function(name, envir) {
>     delayedAssign(
>       name,
>       stop(sprintf("INTERNAL ERROR: %s is not declared",
> sQuote(name)), call. = FALSE),
>       assign.env = envir
>     )
>   }, envir = environment())
>
>   function() {
>     mtcars |> select(mpg, cyl) |> head(3)
>   }
> })
>
> The latter would throw an error, if you actually end up using 'mpg' or
> 'cyl' in a non-NSE way.
>
> /Henrik
>
> On Fri, Oct 7, 2022 at 12:29 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
> >
> > 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://secure-web.cisco.com/1aXcD51cWOTTZe70tiCt6ZRCwUvekoIeEVzYUbBsmd3SAF2biL0Xz4j0btyW2apOx9duGM0EZQoqWUjmigcJoAA6b00uaxgeLzSfgilo-MrXdUTnGVGeCvVcKT0t4HKUFhFlOD5zUpUpYBVZ6yursleQv-rRmLv9jBkwAocGEPrEdGPhcdmRztaKQTX9J-G8EPxM0HV25FuTac5rEbFw6bCd2C7GebbWV-yKqIrlm0f9exsjHVabwnna17diW1vwDN0KNoTWLospRJPNWAi4mzr3oZUu4Xvajyt0GhRtUyDSNwmbvkkRK6w6TusuXVEJY/https%3A%2F%2Fgithub.com%2Fcalabrialab%2FISAnalytics 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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