Re: [R-pkg-devel] HTML validation error in roxygen2 generated documentation
В Thu, 31 Oct 2024 18:04:47 +0100
Nikos Bosse пишет:
> Found the following HTML validation problems:
> ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning:
> inserting implicit
> ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning:
> trimming empty
Thank you for providing the links to the source code!
This can be diagnosed using R CMD Rdconv:
R CMD Rdconv -o ae_median_quantile.html -t html ae_median_quantile.Rd
tidy ae_median_quantile.html >/dev/null
Here are the lines around the problematic part of the HTML document:
---8<---
Input format
---8<---
This is inserted here by Rd2HTML to terminate the paragraph
started above (I think by \figure if not by \section). Rd2HTML doesn't
know that you started and ended a before this line, which
implicitly ended the previous , which makes the present an
error.
The only way I was able to silence the warning while preserving the
existing tag structure was to make it \out{} to start the new
paragraph and provide some text for the auto-inserted to finish
it. Maybe you'll come up with a better fix that doesn't rely on Rd2HTML
auto-inserting the terminating . I'm not sure, but could it help to
set style="text-align: left;..." on \figure itself, without the ?
--
Best regards,
Ivan
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[R-pkg-devel] HTML validation error in roxygen2 generated documentation
Dear list,
I'm trying to submit an updated version of R package scoringutils to CRAN
(https://github.com/epiforecasts/scoringutils). I built the package using `R
CMD build` with Roxygen2 7.3.2 both on Mac and on Ubuntu.
I'm seeing a NOTE related to several HTML validation problems (see below).
These are some of the offending Rd files and corresponding source files:
•
https://github.com/epiforecasts/scoringutils/blob/main/man/ae_median_quantile.Rd,
https://github.com/epiforecasts/scoringutils/blob/efb41afd9925ffc4b62963abc0642cc1f7447c22/R/metrics-quantile.R#L559
• https://github.com/epiforecasts/scoringutils/blob/main/man/dss_sample.Rd,
https://github.com/epiforecasts/scoringutils/blob/efb41afd9925ffc4b62963abc0642cc1f7447c22/R/metrics-sample.R#L224
•
https://github.com/epiforecasts/scoringutils/blob/main/man/interpolate_median.Rd,
https://github.com/epiforecasts/scoringutils/blob/efb41afd9925ffc4b62963abc0642cc1f7447c22/R/metrics-quantile.R#L530
I suspect the issue might be related to images that get added using the
following code
(https://github.com/epiforecasts/scoringutils/blob/efb41afd9925ffc4b62963abc0642cc1f7447c22/R/documentation-templates.R#L106):
```
#' Illustration of required inputs for sample-based forecasts
#' @details # Input format
#' \if{html}{
#' \out{}
#' \figure{metrics-sample.png}{options: style="width:750px;max-width:100\%;"}
#' \out{}
#' }
#' \if{latex}{
#' \figure{metrics-sample.png}
#' }
#' @name illustration-input-metric-sample
#' @keywords internal
NULL
```
I've tried changing @details to @section, tried adding linebreaks, but that
didn't help, unfortunately.
Any help would be much appreciated, thank you!
Best wishes,
Nikos
CRAN Note:
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: HTML version of manual, Result: NOTE
Found the following HTML validation problems:
ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning: inserting
implicit
ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning: trimming
empty
ae_median_sample.html:71:1 (ae_median_sample.Rd:35): Warning: inserting
implicit
ae_median_sample.html:71:1 (ae_median_sample.Rd:35): Warning: trimming empty
bias_quantile.html:133:1 (bias_quantile.Rd:85): Warning: inserting implicit
bias_quantile.html:133:1 (bias_quantile.Rd:85): Warning: trimming empty
bias_sample.html:94:1 (bias_sample.Rd:56): Warning: inserting implicit
bias_sample.html:94:1 (bias_sample.Rd:56): Warning: trimming empty
crps_sample.html:107:1 (crps_sample.Rd:73): Warning: inserting implicit
crps_sample.html:107:1 (crps_sample.Rd:73): Warning: trimming empty
dss_sample.html:70:1 (dss_sample.Rd:35): Warning: inserting implicit
dss_sample.html:70:1 (dss_sample.Rd:35): Warning: trimming empty
get_metrics.forecast_binary.html:82:1 (get_metrics.forecast_binary.Rd:39):
Warning: inserting implicit
get_metrics.forecast_binary.html:82:1 (get_metrics.forecast_binary.Rd:39):
Warning: trimming empty
get_metrics.forecast_point.html:92:1 (get_metrics.forecast_point.Rd:50):
Warning: inserting implicit
get_metrics.forecast_point.html:92:1 (get_metrics.forecast_point.Rd:50):
Warning: trimming empty
get_metrics.forecast_quantile.html:104:1
(get_metrics.forecast_quantile.Rd:52): Warning: inserting implicit
get_metrics.forecast_quantile.html:104:1
(get_metrics.forecast_quantile.Rd:52): Warning: trimming empty
get_metrics.forecast_sample.html:100:1 (get_metrics.forecast_sample.Rd:44):
Warning: inserting implicit
get_metrics.forecast_sample.html:100:1 (get_metrics.forecast_sample.Rd:44):
Warning: trimming empty
get_pairwise_comparisons.html:43:1 (get_pairwise_comparisons.Rd:74): Warning:
inserting implicit
get_pairwise_comparisons.html:43:1 (get_pairwise_comparisons.Rd:74): Warning:
trimming empty
illustration-input-metric-binary-point.html:35:1
(illustration-input-metric-binary-point.Rd:17): Warning: inserting implicit
illustration-input-metric-binary-point.html:35:1
(illustration-input-metric-binary-point.Rd:17): Warning: trimming empty
illustration-input-metric-nominal.html:35:1
(illustration-input-metric-nominal.Rd:17): Warning: inserting implicit
illustration-input-metric-nominal.html:35:1
(illustration-input-metric-nominal.Rd:17): Warning: trimming empty
illustration-input-metric-quantile.html:35:1
(illustration-input-metric-quantile.Rd:17): Warning: inserting implicit
illustration-input-metric-quantile.html:35:1
(illustration-input-metric-quantile.Rd:17): Warning: trimming empty
illustration-input-metric-sample.html:35:1
(illustration-input-metric-sample.Rd:17): Warning: inserting implicit
illustration-input-metric-sample.html:35:1
(illustration-input-metric-sample.Rd:17): Warning: trimming empty
interpolate_median.html:67:1 (interpolate_median.Rd:34): Warning: inserting
implicit
interpolate_median.html:67:1 (interpolate_median.Rd:34): Warning: trimming
empty
interval_coverage.html:83:1 (interval_coverage.Rd:46)
Re: [R-pkg-devel] Warnings related to functions from the survival package
В Thu, 31 Oct 2024 12:06:25 -0400 Kaifeng Lu пишет: > /home/hornik/src/R/src/main/dotcode.c:1978:2: runtime error: call to > function coxph_wtest through pointer to incorrect function type 'void > (*)(void *, void *, void *, void *, void *, void *)' > /home/hornik/src/R/src/main/dotcode.c:1994:2: runtime error: call to > function agsurv5 through pointer to incorrect function type 'void > (*)(void *, void *, void *, void *, void *, void *, void *, void *, > void *, void *)' /home/hornik/src/R/src/main/dotcode.c:2008:2: > runtime error: call to function survdiff2 through pointer to > incorrect function type 'void (*)(void *, void *, void *, void *, > void *, void *, void *, void *, void *, void *, void *, void *, void > *)' /home/hornik/src/R/src/main/dotcode.c:1986:2: runtime error: call > to function coxmart through pointer to incorrect function type 'void > (*)(void *, void *, void *, void *, void *, void *, void *, void *)' This is something R does to call all .C() / .Fortran() functions. For example, coxph_wtest actually takes int*, int*, double*, double*, double*, double *, but R assumes that the calling convention is the same as if it took 6 times void* and calls it through a pointer of a different type [1]. In practice it works well, but formally, calling a function through a pointer of a different type is undefined behaviour. Unfortunately, there is no easy way to call arbitrary functions, like .C() and .Fortran() do, without either breaking some rules (which happens here) or generating function calls at runtime (like some foreign function interfaces do, which is less portable). This check may need suppressions for src/main/dotcode.c or special attributes [2] on R's do_dotCode. -- Best regards, Ivan [1] https://github.com/r-devel/r-svn/blob/91a84c048a26b2b776603482545e4678625a54c3/src/main/dotcode.c#L1977-L1979 [2] https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html#issue-suppression __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings related to functions from the survival package
On 10/31/24 17:39, Ivan Krylov via R-package-devel wrote: В Thu, 31 Oct 2024 12:06:25 -0400 Kaifeng Lu пишет: /home/hornik/src/R/src/main/dotcode.c:1978:2: runtime error: call to function coxph_wtest through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *)' /home/hornik/src/R/src/main/dotcode.c:1994:2: runtime error: call to function agsurv5 through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *)' /home/hornik/src/R/src/main/dotcode.c:2008:2: runtime error: call to function survdiff2 through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *)' /home/hornik/src/R/src/main/dotcode.c:1986:2: runtime error: call to function coxmart through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *, void *, void *)' This is something R does to call all .C() / .Fortran() functions. For example, coxph_wtest actually takes int*, int*, double*, double*, double*, double *, but R assumes that the calling convention is the same as if it took 6 times void* and calls it through a pointer of a different type [1]. In practice it works well, but formally, calling a function through a pointer of a different type is undefined behaviour. Unfortunately, there is no easy way to call arbitrary functions, like .C() and .Fortran() do, without either breaking some rules (which happens here) or generating function calls at runtime (like some foreign function interfaces do, which is less portable). This check may need suppressions for src/main/dotcode.c or special attributes [2] on R's do_dotCode. Yes, yes. This is in base R and can be ignored by package authors. We might consider outsourcing this e.g. to libffi at some point, but for now, if you know an elegant, minimal way how to suppress this, and have the time and energy, a patch would be welcome. We've known about this since the start of this year, but it hasn't gotten high enough on anyone's priority list, and then popped up here. Best Tomas __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Warnings related to functions from the survival package
Dear friends, I received the following warning messages related to functions from the survival package. I didn't directly use the functions mentioned below: coxph_wtest, agsurv5, survdiff2, and coxmart. I believe they are used by higher-level functions from the survival package, such as survdiff and coxph, which I used in my unit tests. Does anyone know how to get rid of suchwarning to pass the CRAN checks? Thank you very much in advance for your help. Regards, Kaifeng package trtswitch_0.1.1.tar.gz does not pass the incoming checks automatically, please see the following pre-tests (additional issue checks): Windows: < https://win-builder.r-project.org/incoming_pretest/trtswitch_0.1.1_20241031_134058/Windows/00check.log > Status: OK Debian: < https://win-builder.r-project.org/incoming_pretest/trtswitch_0.1.1_20241031_134058/Debian/00check.log > Status: OK Additional issues checked: < https://win-builder.r-project.org/incoming_pretest/trtswitch_0.1.1_20241031_134058/specialChecks/ > clang-san: Status: WARNING More details are given in the directory: < https://win-builder.r-project.org/incoming_pretest/trtswitch_0.1.1_20241031_134058/ > The files will be removed after roughly 7 days. Flavor: r-devel-linux-x86_64-debian-special-clang-san Check: *, Result: NA Flavor: r-devel-linux-x86_64-debian-special-clang-san Check: Post-processing issues found for clang-san, Result: WARNING File: tests/testthat.Rout /home/hornik/src/R/src/main/dotcode.c:1978:2: runtime error: call to function coxph_wtest through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *)' /home/hornik/src/R/src/main/dotcode.c:1994:2: runtime error: call to function agsurv5 through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *)' /home/hornik/src/R/src/main/dotcode.c:2008:2: runtime error: call to function survdiff2 through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *)' /home/hornik/src/R/src/main/dotcode.c:1986:2: runtime error: call to function coxmart through pointer to incorrect function type 'void (*)(void *, void *, void *, void *, void *, void *, void *, void *)' [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings related to functions from the survival package
On Thu, 31 Oct 2024 17:59:01 +0100
Tomas Kalibera wrote:
> for now, if you know an elegant, minimal way how to suppress
> this, and have the time and energy, a patch would be welcome
A fresh R-4.4.2 build compiled with clang-19 -fsanitize=function gives
the error:
$ bin/R -q -s -e 'library(survival); survdiff(Surv(futime, fustat) ~
rx,data=ovarian)'
dotcode.c:2008:2: runtime error: call to function survdiff2 through pointer to
incorrect function type 'void (*)(void *, void *, void *, void *, void *, void
*, void *, void *, void *, void *, void *, void *, void *)'
/tmp/RtmpW0SC00/R.INSTALL5d1b3402d0c5/survival/src/survdiff2.c:10: note:
survdiff2 defined here
SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior dotcode.c:2008:2
A suppression file will avoid the error without patching R:
$ cat dotcode.supp
function:dotcode.c
or more fine-grained:
$ cat dotcode.supp
function:do_dotCode
$ UBSAN_OPTIONS="suppressions=$(realpath dotcode.supp)" bin/R -q -s -e
'library(survival); survdiff(Surv(futime, fustat) ~ rx,data=ovarian)'
Call:
survdiff(formula = Surv(futime, fustat) ~ rx, data = ovarian)
Alternatively, the following patch will also suppress the error:
--- src/main/dotcode.c 2024-03-26 23:02:08.0 +
+++ src/main/dotcode.c 2024-10-31 19:53:36.272334541 +
@@ -1658,6 +1658,9 @@
#define FILL 0xee
#define NG 64
+#ifdef __clang__
+__attribute__((no_sanitize("function")))
+#endif
attribute_hidden SEXP do_dotCode(SEXP call, SEXP op, SEXP args, SEXP env)
{
void **cargs, **cargs0 = NULL /* -Wall */;
I hope I understood you correctly that you're looking for a tested
workaround.
--
Best regards,
Ivan
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Re: [R-pkg-devel] HTML validation error in roxygen2 generated documentation
Hi Ivan,
Thanks SO much for your quick help. Removing the did not work. However, I
now did
```
#' \if{html}{
#' \out{}
#' \figure{metrics-binary-point.png}{options:
style="width:750px;max-width:100\%;"}
#' \out{}
#' Overview of required input format for binary and point forecasts
#' }
```
with an addition and some text, following your suggestion. And that worked
like a charm. Also thank your for showing me R CMD Rdconv.
You made my day!
With gratitude and best regards,
Nikos
On 31 Oct 2024 at 19:06 +0100, Ivan Krylov , wrote:
> В Thu, 31 Oct 2024 18:04:47 +0100
> Nikos Bosse пишет:
>
> > Found the following HTML validation problems:
> > ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning:
> > inserting implicit
> > ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning:
> > trimming empty
>
> Thank you for providing the links to the source code!
>
> This can be diagnosed using R CMD Rdconv:
>
> R CMD Rdconv -o ae_median_quantile.html -t html ae_median_quantile.Rd
> tidy ae_median_quantile.html >/dev/null
>
> Here are the lines around the problematic part of the HTML document:
>
> ---8<---
> Input format
>
>
>
> style="width:750px;max-width:100%;" alt="metrics-quantile.png" />
>
>
>
> ---8<---
>
> This is inserted here by Rd2HTML to terminate the paragraph
> started above (I think by \figure if not by \section). Rd2HTML doesn't
> know that you started and ended a before this line, which
> implicitly ended the previous , which makes the present an
> error.
>
> The only way I was able to silence the warning while preserving the
> existing tag structure was to make it \out{} to start the new
> paragraph and provide some text for the auto-inserted to finish
> it. Maybe you'll come up with a better fix that doesn't rely on Rd2HTML
> auto-inserting the terminating . I'm not sure, but could it help to
> set style="text-align: left;..." on \figure itself, without the ?
>
> --
> Best regards,
> Ivan
[[alternative HTML version deleted]]
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