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-boun...@r-project.org> on behalf of Sergio Oller
<sergiol...@gmail.com>
Sent: Saturday, October 8, 2022 4:38 AM
To: bioc-devel@r-project.org <bioc-devel@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.bengts...@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.b...@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-boun...@r-project.org> on behalf of Marcel
> Ramos <marcel.ramospe...@roswellpark.org>
> > Date: Friday, October 7, 2022 at 3:07 PM
> > To: bioc-devel@r-project.org <bioc-devel@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-boun...@r-project.org> on behalf of
> > > Marcel Ramos <marcel.ramospe...@roswellpark.org>
> > > *Date: *Wednesday, 2022October5 at 23:48
> > > *To: *bioc-devel@r-project.org <bioc-devel@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]]
> > > >
> > > >
> > > > _______________________________________________
> > > > Bioc-devel@r-project.org mailing list
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