Re: [Rd] BUG?: R CMD check with --as-cran *disables* checks for unused imports otherwise performed
I've just posted this to BugZilla as PR18229
(https://bugs.r-project.org/show_bug.cgi?id=18229) to make sure it's
tracked.
/Henrik
On Wed, Oct 20, 2021 at 8:08 PM Jeffrey Dick wrote:
>
> FWIW, I also encountered this issue and posted on R-pkg-devel about it, with
> no resolution at the time (May 2020). See "Dependencies NOTE lost with
> --as-cran" (https://stat.ethz.ch/pipermail/r-package-devel/2020q2/005467.html)
>
> On Wed, Oct 20, 2021 at 11:55 PM Henrik Bengtsson
> wrote:
>>
>> ISSUE:
>>
>> Using 'R CMD check' with --as-cran,
>> set_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_=TRUE, whereas the
>> default is FALSE, which you get if you don't add --as-cran.
>> I would expect --as-cran to check more things and more be conservative
>> than without. So, is this behavior a mistake? Could it be a thinko
>> around the negating "IGNORE", and the behavior is meant to be vice
>> verse?
>>
>> Example:
>>
>> $ R CMD check QDNAseq_1.29.4.tar.gz
>> ...
>> * using R version 4.1.1 (2021-08-10)
>> * using platform: x86_64-pc-linux-gnu (64-bit)
>> ...
>> * checking dependencies in R code ... NOTE
>> Namespace in Imports field not imported from: ‘future’
>> All declared Imports should be used.
>>
>> whereas, if I run with --as-cran, I don't get that NOTE;
>>
>> $ R CMD check --as-cran QDNAseq_1.29.4.tar.gz
>> ...
>> * checking dependencies in R code ... OK
>>
>>
>> TROUBLESHOOTING:
>>
>> In src/library/tools/R/check.R [1], the following is set if --as-cran is
>> used:
>>
>> Sys.setenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_" = "TRUE")
>>
>> whereas, if not set, the default is:
>>
>> ignore_unused_imports <-
>> config_val_to_logical(Sys.getenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_",
>> "FALSE"))
>>
>> [1]
>> https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/check.R#L6335
>> [2]
>> https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/QC.R#L5954-L5956
>>
>> /Henrik
>>
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Re: [Rd] BUG?: R CMD check with --as-cran *disables* checks for unused imports otherwise performed
FWIW, I also encountered this issue and posted on R-pkg-devel about it,
with no resolution at the time (May 2020). See "Dependencies NOTE lost with
--as-cran" (
https://stat.ethz.ch/pipermail/r-package-devel/2020q2/005467.html)
On Wed, Oct 20, 2021 at 11:55 PM Henrik Bengtsson <
henrik.bengts...@gmail.com> wrote:
> ISSUE:
>
> Using 'R CMD check' with --as-cran,
> set_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_=TRUE, whereas the
> default is FALSE, which you get if you don't add --as-cran.
> I would expect --as-cran to check more things and more be conservative
> than without. So, is this behavior a mistake? Could it be a thinko
> around the negating "IGNORE", and the behavior is meant to be vice
> verse?
>
> Example:
>
> $ R CMD check QDNAseq_1.29.4.tar.gz
> ...
> * using R version 4.1.1 (2021-08-10)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> ...
> * checking dependencies in R code ... NOTE
> Namespace in Imports field not imported from: ‘future’
> All declared Imports should be used.
>
> whereas, if I run with --as-cran, I don't get that NOTE;
>
> $ R CMD check --as-cran QDNAseq_1.29.4.tar.gz
> ...
> * checking dependencies in R code ... OK
>
>
> TROUBLESHOOTING:
>
> In src/library/tools/R/check.R [1], the following is set if --as-cran is
> used:
>
> Sys.setenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_" = "TRUE")
>
> whereas, if not set, the default is:
>
> ignore_unused_imports <-
>
> config_val_to_logical(Sys.getenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_",
> "FALSE"))
>
> [1]
> https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/check.R#L6335
> [2]
> https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/QC.R#L5954-L5956
>
> /Henrik
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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[Rd] BUG?: R CMD check with --as-cran *disables* checks for unused imports otherwise performed
ISSUE:
Using 'R CMD check' with --as-cran,
set_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_=TRUE, whereas the
default is FALSE, which you get if you don't add --as-cran.
I would expect --as-cran to check more things and more be conservative
than without. So, is this behavior a mistake? Could it be a thinko
around the negating "IGNORE", and the behavior is meant to be vice
verse?
Example:
$ R CMD check QDNAseq_1.29.4.tar.gz
...
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
...
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘future’
All declared Imports should be used.
whereas, if I run with --as-cran, I don't get that NOTE;
$ R CMD check --as-cran QDNAseq_1.29.4.tar.gz
...
* checking dependencies in R code ... OK
TROUBLESHOOTING:
In src/library/tools/R/check.R [1], the following is set if --as-cran is used:
Sys.setenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_" = "TRUE")
whereas, if not set, the default is:
ignore_unused_imports <-
config_val_to_logical(Sys.getenv("_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_",
"FALSE"))
[1]
https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/check.R#L6335
[2]
https://github.com/wch/r-source/blob/b50e3f755674cbb697a4a7395b766647a5cfeea2/src/library/tools/R/QC.R#L5954-L5956
/Henrik
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