Re: [R-pkg-devel] how to change from -fsanitize=undefined to -fsanitize=address

[Youyi Fong]

Here is a solution worked out by the wonderful staff from our scientific
computing support team at the Fred Hutchinson Cancer Research Center. I
really don't know how Dan did it, but the way he explained to me was that
he came across this github repository by Dirk:
https://github.com/rocker-org/r-devel-san-clang. There was the Docker file
which built the clang-san image, but he did not find the image itself in
Docker Hub. So he built it himself and pushed it as
dtenenba/r-devel-san-clang.

The issue I encountered with r-debug was related to ulimit. It turns out
that it be specific to the machine I was working on. Dan used a different
machine and that went away.

Using the docker image dtenenba/r-devel-san-clang on that new machine, I
was able to install my package, and upon running the test code, to
reproduce the memory issue reported by the CRAN team.

I then tested whether r-debug might also work on that machine. It sort of
did as it returned a memory-related error when I tried

RDsan CMD INSTALL mypkg

But it is not as helpful as the behavior by  dtenenba/r-devel-san-clang.




On Fri, Nov 29, 2019 at 1:48 PM Youyi Fong  wrote:

> Hi Dirk,
>
> Thanks very much. Following your suggestion, I tried r-debug, following
> the readme on https://github.com/wch/r-debug. After starting docker as
> recommended,
>
> docker run --rm -ti --security-opt seccomp=unconfined wch1/r-debug
>
> I was able to call RD. But calling RDsan or RDcsan resulted in errors:
>
> root@258bfdfcce6c:/# RDsan
> ==17==ERROR: AddressSanitizer failed to allocate 0xdfff0001000
> (15392894357504) bytes at address 2008fff7000 (errno: 12)
> ==17==ReserveShadowMemoryRange failed while trying to map 0xdfff0001000
> bytes. Perhaps you're using ulimit -v
> Aborted (core dumped)
>
>
> I have also tried rhub before, following this article:
> https://cran.r-project.org/web/packages/rhub/vignettes/local-debugging.html As
> you indicated, it may have worked for others, but got the following error:
>
> > Installing system requirements
> 3b3a65d751c026b7629d2038242c92290cf97853525978381b6e59f41c8500d3
>
> > Starting Docker container
> 04d6065323ef732bf89c26df7d547efff40774206a0ac6a24b3d9cdb021cb08e
> ls: cannot access '/opt/R-*': No such file or directory
> > source('https://bioconductor.org/biocLite.R')
> Error: With R version 3.5 or greater, install Bioconductor packages using
> BiocManager; see https://bioconductor.org/install
> Execution halted
> Error in run(bash, c(file.path(wd, "rhub-linux.sh"), args), echo = TRUE,  :
>   System command error
>
>
>
> This is where I am stuck at right now.
>
> Thanks,
> Youyi
>
>
> On Fri, Nov 29, 2019 at 10:46 AM Dirk Eddelbuettel  wrote:
>
>>
>> Youyi,
>>
>> It looks like you are trying to debug a _current_ SAN / ASAN / UBSAN error
>> against your package by leaning on documentation I wrote five years ago
>> specifically for another package (called "sanitizers") used to validate
>> the
>> initial Docker container builds I made (and to ensure the error these
>> SAN/ASAN/UBSAN containers were supposed to trigger were triggered).
>>
>> Today, your quickest bet to launch a sanitizer run may be via the rhub
>> platforms.  Clearly the easiest to launch ("no download"), but at times a
>> little inconsistent.  An alternative is the suite of containers
>> maintained by
>> Winston described at their repo at https://github.com/wch/r-debug at
>> available from the Docker Hub.
>>
>> All that said, exact configurations matters and the fact remains that we
>> all
>> still haven't managed to automatically provide the configurations used by
>> CRAN. There are possible "gaps" between what CRAN uses and what may be
>> available pre-built: compiler versions, builds, sanitizer options, ... and
>> these can be enough to not replicate an issue.  I think I would try
>> Winston's
>> r-debug next.
>>
>> Hope this helps, Dirk
>>
>> --
>> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>>
>

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Re: [R-pkg-devel] casen 0.1: strange pre-test results

[Uwe Ligges]

Pls ignore the knitr et all missings for now, some hicc up on the check 
machine caused an inconsistent setup. We will fix this shortly.


Best,
Uwe Ligges

On 01.12.2019 00:06, Dirk Eddelbuettel wrote:


On 30 November 2019 at 18:29, Mauricio Vargas wrote:
| This is the 1st time that the pre-checks shows strange errors for me. The
| results are here
| 
https://win-builder.r-project.org/incoming_pretest/casen_0.1.0.9000_20191130_185019/

Following that URL to

   
https://win-builder.r-project.org/incoming_pretest/casen_0.1.0.9000_20191130_185019/Debian/00install.out

we see a different, and fatal, error:

   * installing *source* package ‘casen’ ...
   ** using staged installation
   'config' variable 'CXXCPP' is deprecated
   PKG_CFLAGS=
   PKG_LIBS=-larchive
   :1:10: fatal error: archive.h: No such file or directory
   compilation terminated.

You are depending on an external library that appears to NOT be installed.

Your package is unlikely to succeed in the build, whether or not knitr and
tidyr are present.

Dirk



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Re: [R-pkg-devel] casen 0.1: strange pre-test results

[Dirk Eddelbuettel]

On 30 November 2019 at 18:29, Mauricio Vargas wrote:
| This is the 1st time that the pre-checks shows strange errors for me. The
| results are here
| 
https://win-builder.r-project.org/incoming_pretest/casen_0.1.0.9000_20191130_185019/

Following that URL to

  
https://win-builder.r-project.org/incoming_pretest/casen_0.1.0.9000_20191130_185019/Debian/00install.out

we see a different, and fatal, error:

  * installing *source* package ‘casen’ ...
  ** using staged installation
  'config' variable 'CXXCPP' is deprecated
  PKG_CFLAGS=
  PKG_LIBS=-larchive
  :1:10: fatal error: archive.h: No such file or directory
  compilation terminated.

You are depending on an external library that appears to NOT be installed.

Your package is unlikely to succeed in the build, whether or not knitr and
tidyr are present.

Dirk

-- 
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[R-pkg-devel] casen 0.1: strange pre-test results

[Mauricio Vargas]

Hi!

This is the 1st time that the pre-checks shows strange errors for me. The
results are here
https://win-builder.r-project.org/incoming_pretest/casen_0.1.0.9000_20191130_185019/

It says, that knitr and tidyr are not available, etc. After testing on
windows, ubuntu and mac, I only have 1 note about a function that reads rar
files.

Here are my test results
https://github.com/pachamaltese/casen/commit/bc4c2c35a1c310dde99d612599da6c72feff5d42/checks?check_suite_id=335739582
so I'm not sure about these pre-test errors.

How would you fix them? so far, my biggest expertise is stackoverflow and
it's not helping at the present time

Best,


—

*Mauricio Vargas Sepúlveda 帕夏*
Do you like Data Science? visit pacha.hk
你爱科学数据专吗？你走pacha.hk

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Re: [R-pkg-devel] bioRxiv Preprint as Vignette

[Dirk Eddelbuettel]

On 30 November 2019 at 19:55, Charith Karunarathna wrote:
| I am just wondering about how I can include a bioRxiv preprint as the 
vignette of my R package. It's a pdf file already in bioRxiv. Could you please 
let me know how I can include that file as vignette?

Sure. "Just do it" -- in the sense that you can create five-line Sweave
vignette wrappers around existing pdf files.  See

  
https://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/

I do the same now in a number of packages, for example my anytime repo

  https://github.com/eddelbuettel/anytime/tree/master/vignettes

Dirk

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Re: [R-pkg-devel] bioRxiv Preprint as Vignette

[Henrik Bengtsson]

Disclaimer, I'm the author: You can include a static PDF using the
R.rsp::asis vignette engine:

  
https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf

Better is if you've got the LaTeX source (with figures etc.), then use
the R.rsp::tex vignette engine:

  
https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-LaTeX_vignettes.pdf

/Henrik

PS. On a side, should LaTeX-to-PDF (as in R.rsp::tex) be part of base
R?  That seems non-controversial to me.  In contrast, including static
PDFs and HTMLs requires a debate whether this is a good thing or not,
e.g. the risk of decoupling/losing the original source artifact and
it's only the final PDF/HTML artifact that is archived on CRAN.

On Sat, Nov 30, 2019 at 11:56 AM Charith Karunarathna
 wrote:
>
> Hi,
>
>
> I am just wondering about how I can include a bioRxiv preprint as the 
> vignette of my R package. It's a pdf file already in bioRxiv. Could you 
> please let me know how I can include that file as vignette?
>
>
> Thank you in advance!
>
>
> Charith.
>
>
>
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>
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[R-pkg-devel] bioRxiv Preprint as Vignette

[Charith Karunarathna]

Hi,


I am just wondering about how I can include a bioRxiv preprint as the vignette 
of my R package. It's a pdf file already in bioRxiv. Could you please let me 
know how I can include that file as vignette?


Thank you in advance!


Charith.



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Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Yoni]

Thank you for the clarification regarding roxygen2, it does look like a
confounding issue.

I will try to resolve the paths in the tex.

Thank you for the help.

On Sat, Nov 30, 2019 at 11:39 AM Iñaki Ucar  wrote:

>
>
> El sáb., 30 nov. 2019 16:22, Yoni  escribió:
>
>> Thank you for the clarification.
>>
>> I am then more confused.
>>
>> The CRAN version of the package (texPreview) has been unchanged since Oct
>> 23, at which point it was passing the checks with no errors.
>>
>
> If your package is sitting on CRAN since then, and in fact I see in your
> DESCRIPTION that you generated the docs with roxygen2 6.1.1, then the
> roxygen2 update has nothing to do with your check error. You run roxygen2;
> CRAN doesn't.
>
> Iñaki
>


-- 
Yoni

You do not learn to swim from books and lectures on the theory of buoyancy
(Box 1990)

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Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Iñaki Ucar]

El sáb., 30 nov. 2019 16:22, Yoni  escribió:

> Thank you for the clarification.
>
> I am then more confused.
>
> The CRAN version of the package (texPreview) has been unchanged since Oct
> 23, at which point it was passing the checks with no errors.
>

If your package is sitting on CRAN since then, and in fact I see in your
DESCRIPTION that you generated the docs with roxygen2 6.1.1, then the
roxygen2 update has nothing to do with your check error. You run roxygen2;
CRAN doesn't.

Iñaki

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Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Duncan Murdoch]

On 30/11/2019 10:21 a.m., Yoni wrote:

Thank you for the clarification.

I am then more confused.

The CRAN version of the package (texPreview) has been unchanged since 
Oct 23, at which point it was passing the checks with no errors.


Here is the CRAN mirror on GitHub with the example that is now erroring.

https://github.com/cran/texPreview/blob/master/R/kable.R

The examples section seems to have valid R code in them.

Last week (after roxygen2 was updated on CRAN to 7.0.1) the same 
documentation is throwing errors.


Here is the CRAN checks link: 
https://cran.r-project.org/web/checks/check_results_texPreview.html


Has the method of checking documentation changed in the past week that 
would cause these previously working examples to start to fail?


I don't really know what the cause is, but I suspect the roxygen2 update 
is a coincidence. In your CRAN log you show this error:


> x <- tex_preview(tex,returnType = 'input')
Error in tex_preview.default(obj, tex_lines, stem, overwrite, 
keep_pdf, :


! LaTeX Error: File `/tmp/Rtmp6V8kds/tex_temp.tex ' not found.

Type X to quit or  to proceed,
or enter new name. (Default extension: tex )

Enter file name:
! Emergency stop.


l.17 \input{ /tmp/Rtmp6V8kds/tex_temp.tex }


If I look really closely at the LaTeX error message, I see that the 
filename has a space at the end.  Your \input macro had spaces both 
before and after.  Perhaps a LaTeX update makes the trailing space 
significant, and that's the issue?  I couldn't spot where those spaces 
came from; maybe if you just remove them the problem will go away.


Duncan Murdoch

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Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Yoni]

Thank you for the clarification.

I am then more confused.

The CRAN version of the package (texPreview) has been unchanged since Oct
23, at which point it was passing the checks with no errors.

Here is the CRAN mirror on GitHub with the example that is now erroring.

https://github.com/cran/texPreview/blob/master/R/kable.R

The examples section seems to have valid R code in them.

Last week (after roxygen2 was updated on CRAN to 7.0.1) the same
documentation is throwing errors.

Here is the CRAN checks link:
https://cran.r-project.org/web/checks/check_results_texPreview.html

Has the method of checking documentation changed in the past week that
would cause these previously working examples to start to fail?

Thank you for the help

On Sat, Nov 30, 2019 at 10:09 AM Duncan Murdoch 
wrote:

> On 30/11/2019 9:59 a.m., Yoni wrote:
> > Thank you for the advice.
> >
> > I think that (a) is a problem to implement since the new roxygen2 is on
> the
> > CRAN systems and I can not control which version they are using to build
> > the package in the checks.
>
> I don't think CRAN runs roxygen2 at all.  It tests based on the
> description of documentation in Writing R Extensions.
>
> Duncan Murdoch
>
> >
> > I have gone with option (c), which is unfortunate since I will need to
> > change my examples twice to accommodate a problem that another package,
> > that has such a high degree of reverse dependency, has created.
> >
> >
> > On Sat, Nov 30, 2019 at 9:42 AM Hugh Parsonage  >
> > wrote:
> >
> >> You could (a) install the updated roxygen from github and rebuild the
> man/
> >> files ; (b) manually edit the Rd files without using roxygen ; or (c)
> >> remove the examples until you can apply the fix.
> >>
> >> On Sun, 1 Dec 2019 at 1:26 am, Yoni  wrote:
> >>
> >>> I received a message from CRAN yesterday stating my package is
> erroring on
> >>> all the systems all of a sudden.
> >>>
> >>> https://cran.r-project.org/web/checks/check_results_texPreview.html
> >>>
> >>> After some investigation the root of the errors looks like it came from
> >>> the
> >>> new release of roxygen2 (7.0.1).
> >>>
> >>> https://github.com/r-lib/roxygen2/issues/990
> >>>
> >>> Is there anything I can do in the interim to fix this problem since I
> do
> >>> not know when this apparent bug fix will be pushed to CRAN, relieving
> my
> >>> errors in the documentation builds, which could be beyond the warning
> >>> period (2019-12-13), which the package will be removed from CRAN.
> >>>
> >>> Thank you
> >>>
> >>>  [[alternative HTML version deleted]]
> >>>
> >>> __
> >>> R-package-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>>
> >>
> >
>
>

-- 
Yoni

You do not learn to swim from books and lectures on the theory of buoyancy
(Box 1990)

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Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Duncan Murdoch]

On 30/11/2019 9:59 a.m., Yoni wrote:

Thank you for the advice.

I think that (a) is a problem to implement since the new roxygen2 is on the
CRAN systems and I can not control which version they are using to build
the package in the checks.


I don't think CRAN runs roxygen2 at all.  It tests based on the 
description of documentation in Writing R Extensions.


Duncan Murdoch



I have gone with option (c), which is unfortunate since I will need to
change my examples twice to accommodate a problem that another package,
that has such a high degree of reverse dependency, has created.


On Sat, Nov 30, 2019 at 9:42 AM Hugh Parsonage 
wrote:


You could (a) install the updated roxygen from github and rebuild the man/
files ; (b) manually edit the Rd files without using roxygen ; or (c)
remove the examples until you can apply the fix.

On Sun, 1 Dec 2019 at 1:26 am, Yoni  wrote:


I received a message from CRAN yesterday stating my package is erroring on
all the systems all of a sudden.

https://cran.r-project.org/web/checks/check_results_texPreview.html

After some investigation the root of the errors looks like it came from
the
new release of roxygen2 (7.0.1).

https://github.com/r-lib/roxygen2/issues/990

Is there anything I can do in the interim to fix this problem since I do
not know when this apparent bug fix will be pushed to CRAN, relieving my
errors in the documentation builds, which could be beyond the warning
period (2019-12-13), which the package will be removed from CRAN.

Thank you

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Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Yoni]

Thank you for the advice.

I think that (a) is a problem to implement since the new roxygen2 is on the
CRAN systems and I can not control which version they are using to build
the package in the checks.

I have gone with option (c), which is unfortunate since I will need to
change my examples twice to accommodate a problem that another package,
that has such a high degree of reverse dependency, has created.


On Sat, Nov 30, 2019 at 9:42 AM Hugh Parsonage 
wrote:

> You could (a) install the updated roxygen from github and rebuild the man/
> files ; (b) manually edit the Rd files without using roxygen ; or (c)
> remove the examples until you can apply the fix.
>
> On Sun, 1 Dec 2019 at 1:26 am, Yoni  wrote:
>
>> I received a message from CRAN yesterday stating my package is erroring on
>> all the systems all of a sudden.
>>
>> https://cran.r-project.org/web/checks/check_results_texPreview.html
>>
>> After some investigation the root of the errors looks like it came from
>> the
>> new release of roxygen2 (7.0.1).
>>
>> https://github.com/r-lib/roxygen2/issues/990
>>
>> Is there anything I can do in the interim to fix this problem since I do
>> not know when this apparent bug fix will be pushed to CRAN, relieving my
>> errors in the documentation builds, which could be beyond the warning
>> period (2019-12-13), which the package will be removed from CRAN.
>>
>> Thank you
>>
>> [[alternative HTML version deleted]]
>>
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>

-- 
Yoni

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(Box 1990)

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Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Hugh Parsonage]

You could (a) install the updated roxygen from github and rebuild the man/
files ; (b) manually edit the Rd files without using roxygen ; or (c)
remove the examples until you can apply the fix.

On Sun, 1 Dec 2019 at 1:26 am, Yoni  wrote:

> I received a message from CRAN yesterday stating my package is erroring on
> all the systems all of a sudden.
>
> https://cran.r-project.org/web/checks/check_results_texPreview.html
>
> After some investigation the root of the errors looks like it came from the
> new release of roxygen2 (7.0.1).
>
> https://github.com/r-lib/roxygen2/issues/990
>
> Is there anything I can do in the interim to fix this problem since I do
> not know when this apparent bug fix will be pushed to CRAN, relieving my
> errors in the documentation builds, which could be beyond the warning
> period (2019-12-13), which the package will be removed from CRAN.
>
> Thank you
>
> [[alternative HTML version deleted]]
>
> __
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[R-pkg-devel] roxygen2 7.0.1 backslash escape error

[Yoni]

I received a message from CRAN yesterday stating my package is erroring on
all the systems all of a sudden.

https://cran.r-project.org/web/checks/check_results_texPreview.html

After some investigation the root of the errors looks like it came from the
new release of roxygen2 (7.0.1).

https://github.com/r-lib/roxygen2/issues/990

Is there anything I can do in the interim to fix this problem since I do
not know when this apparent bug fix will be pushed to CRAN, relieving my
errors in the documentation builds, which could be beyond the warning
period (2019-12-13), which the package will be removed from CRAN.

Thank you

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Re: [R-pkg-devel] winOS devel failure "knitr not available" on resubmit

[Duncan Murdoch]

On 30/11/2019 9:05 a.m., Yoni wrote:

Thank you for the advice.

I resubmitted to win-devel 20 minutes ago (0840 EST) and that error 
seems to be persisting.


https://win-builder.r-project.org/Htqi1hmm4O20/00check.log

here is the link to the full DESCRIPTION file

https://raw.githubusercontent.com/yonicd/ripe/master/DESCRIPTION


It looks like a problem on win-builder.  I don't think there's anything 
you can do but wait for it to be fixed.




That is the same system that CRAN checks for winOS will use?


I don't know, but I'd expect so.

Duncan Murdoch



Thank you

On Sat, Nov 30, 2019 at 8:29 AM Duncan Murdoch > wrote:


On 30/11/2019 7:02 a.m., Yoni wrote:
 > I have recently resubmitted a package after fixing an issue with the
 > license. The package passed all the checks a few days prior and
on this
 > resubmit the winOS failed with a message that I am not sure how
to resolve.
 >
 > * checking package dependencies ... ERROR
 > Package suggested but not available for checking:
 > 'knitr'VignetteBuilder package required for checking but not
 > installed: 'knitr'
 >
 >

https://win-builder.r-project.org/incoming_pretest/ripe_0.1.0_20191130_120421/Windows/00check.log
 >
 > The DESCRIPTION file seems to contain the correct Imports and
Suggests
 > that have not raised issues up until this point on checks.Depends: R
 > (>= 3.5.0)
 >
 > Imports: magrittrSuggests:
 >   testthat,
 >   knitr,
 >   rmarkdown,
 >   purrr,
 >   parallel,
 >   dplyr,
 >   covr
 > VignetteBuilder: knitr
 >

Assuming the joined lines "Imports: magrittrSuggests:" are just in your
email, not in the DESCRIPTION file (you used HTML, which generally gets
mangled here), that's likely a transient error on the test system.  I
would resubmit.

Duncan Murdoch



--
Yoni

You do not learn to swim from books and lectures on the theory of 
buoyancy (Box 1990)


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Re: [R-pkg-devel] winOS devel failure "knitr not available" on resubmit

[Yoni]

Thank you for the advice.

I resubmitted to win-devel 20 minutes ago (0840 EST) and that error seems
to be persisting.

https://win-builder.r-project.org/Htqi1hmm4O20/00check.log

here is the link to the full DESCRIPTION file

https://raw.githubusercontent.com/yonicd/ripe/master/DESCRIPTION

That is the same system that CRAN checks for winOS will use?

Thank you

On Sat, Nov 30, 2019 at 8:29 AM Duncan Murdoch 
wrote:

> On 30/11/2019 7:02 a.m., Yoni wrote:
> > I have recently resubmitted a package after fixing an issue with the
> > license. The package passed all the checks a few days prior and on this
> > resubmit the winOS failed with a message that I am not sure how to
> resolve.
> >
> > * checking package dependencies ... ERROR
> > Package suggested but not available for checking:
> > 'knitr'VignetteBuilder package required for checking but not
> > installed: 'knitr'
> >
> >
> https://win-builder.r-project.org/incoming_pretest/ripe_0.1.0_20191130_120421/Windows/00check.log
> >
> > The DESCRIPTION file seems to contain the correct Imports and Suggests
> > that have not raised issues up until this point on checks.Depends: R
> > (>= 3.5.0)
> >
> > Imports: magrittrSuggests:
> >   testthat,
> >   knitr,
> >   rmarkdown,
> >   purrr,
> >   parallel,
> >   dplyr,
> >   covr
> > VignetteBuilder: knitr
> >
>
> Assuming the joined lines "Imports: magrittrSuggests:" are just in your
> email, not in the DESCRIPTION file (you used HTML, which generally gets
> mangled here), that's likely a transient error on the test system.  I
> would resubmit.
>
> Duncan Murdoch
>


-- 
Yoni

You do not learn to swim from books and lectures on the theory of buoyancy
(Box 1990)

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Re: [R-pkg-devel] winOS devel failure "knitr not available" on resubmit

[Duncan Murdoch]

On 30/11/2019 7:02 a.m., Yoni wrote:

I have recently resubmitted a package after fixing an issue with the
license. The package passed all the checks a few days prior and on this
resubmit the winOS failed with a message that I am not sure how to resolve.

* checking package dependencies ... ERROR
Package suggested but not available for checking:
'knitr'VignetteBuilder package required for checking but not
installed: 'knitr'

https://win-builder.r-project.org/incoming_pretest/ripe_0.1.0_20191130_120421/Windows/00check.log

The DESCRIPTION file seems to contain the correct Imports and Suggests
that have not raised issues up until this point on checks.Depends: R
(>= 3.5.0)

Imports: magrittrSuggests:
  testthat,
  knitr,
  rmarkdown,
  purrr,
  parallel,
  dplyr,
  covr
VignetteBuilder: knitr



Assuming the joined lines "Imports: magrittrSuggests:" are just in your 
email, not in the DESCRIPTION file (you used HTML, which generally gets 
mangled here), that's likely a transient error on the test system.  I 
would resubmit.


Duncan Murdoch

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[R-pkg-devel] winOS devel failure "knitr not available" on resubmit

[Yoni]

I have recently resubmitted a package after fixing an issue with the
license. The package passed all the checks a few days prior and on this
resubmit the winOS failed with a message that I am not sure how to resolve.

* checking package dependencies ... ERROR
Package suggested but not available for checking:
'knitr'VignetteBuilder package required for checking but not
installed: 'knitr'

https://win-builder.r-project.org/incoming_pretest/ripe_0.1.0_20191130_120421/Windows/00check.log

The DESCRIPTION file seems to contain the correct Imports and Suggests
that have not raised issues up until this point on checks.Depends: R
(>= 3.5.0)

Imports: magrittrSuggests:
 testthat,
 knitr,
 rmarkdown,
 purrr,
 parallel,
 dplyr,
 covr
VignetteBuilder: knitr

Thank you

Yoni

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