Re: [R-pkg-devel] Updating package with a dependency (rJava) that doesn't build on all flavours

2020-01-16 Thread Tomáš Kliegr
Hi,

This issue has been apparently solved: https://github.com/s-u/rJava/issues/203


Tomas

Od: R-package-devel  za uživatele Tomáš 
Kliegr 
Odesláno: pátek 29. listopadu 2019 15:40
Komu: r-package-devel@r-project.org 
Předmět: Re: [R-pkg-devel] Updating package with a dependency (rJava) that 
doesn't build on all flavours

Hi,

Just a brief update: It seems that this problem still persists and indeed 
prevents updates of multiple packages in CRAN.
I, therefore, setup a GitHub issue for it here: 
https://github.com/s-u/rJava/issues/203#issuecomment-557927860

Tomas




Od: R-package-devel  za uživatele Tomáš 
Kliegr 
Odesláno: čtvrtek 14. listopadu 2019 16:52
Komu: Kevin Kuo ; r-package-devel@r-project.org 

Předmět: Re: [R-pkg-devel] Updating package with a dependency (rJava) that 
doesn't build on all flavours

Hi,

>https://stat.ethz.ch/pipermail/r-package-devel/2019q4/004539.html

Yes, it is almost certainly the same issue as this one reported in October 
2019. It seems that the policy must have changed sometime around September. As 
follows from "Reverse depends" of rJava, packages depending on rJava were 
successfully updated in mid-2019. The most recently updated package was 
apparently Crossover in May 2019.

Tomas

Od: R-package-devel  za uživatele Kevin 
Kuo 
Odesláno: středa 13. listopadu 2019 19:54
Komu: r-package-devel@r-project.org 
Předmět: Re: [R-pkg-devel] Updating package with a dependency (rJava) that 
doesn't build on all flavours

FYI see also
https://stat.ethz.ch/pipermail/r-package-devel/2019q4/004539.html

On Wed, Nov 13, 2019 at 10:52 AM Tomáš Kliegr  wrote:

> Hi,
>
> >This is probably a temporary Java installation problem on a CRAN Windows
> machine, cran-submissi...@r-project.org is the right place to report
> this, please be patient.
>
> I am  not sure this is the case, to me it looks like a recent policy
> change. The rJava builds were not going through on this particular machine
> for quite some time, and this had no effect on the updates of packages
> depending on rJava being accepted. Now, they seem to get automatically
> rejected. Regarding the email to cran-submissi...@r-project.org, I sent
> it a week ago, but maybe this just takes longer than I though.. will wait,
>
> It is also possible that I am overlooking something important...
>
> Best,
>
> Tomas
>
> 
> Od: Tomas Kalibera 
> Odesláno: středa 13. listopadu 2019 11:03
> Komu: Tomáš Kliegr ; r-package-devel@r-project.org <
> r-package-devel@r-project.org>
> Předmět: Re: [R-pkg-devel] Updating package with a dependency (rJava) that
> doesn't build on all flavours
>
> On 11/13/19 10:19 AM, Tomáš Kliegr wrote:
> > Hello,
> >
> > This question has not stirred much discussion ... If this is the wrong
> place to ask,  I was wondering if some one point me to where I should ask,
> or who to approach?  If I understand this issue correctly, it does not
> affect only my package, but also the maintainers of 50+ other packages that
> depend on rJava when they will try to update the package.
> >
> > So far I tried putting the explanation to the comment field when
> submitting the update, and I also tried emailing
> cran-submissi...@r-project.org, but that was also without response so far.
>
> This is probably a temporary Java installation problem on a CRAN Windows
> machine, cran-submissi...@r-project.org is the right place to report
> this, please be patient.
>
> Thanks
> Tomas
>
> >
> > Thanks for any pointers,
> >
> > Tomas
> > 
> > Od: R-package-devel  za
> uživatele Tomáš Kliegr 
> > Odesláno: pondělí 11. listopadu 2019 11:09
> > Komu: r-package-devel@r-project.org 
> > Předmět: [R-pkg-devel] Updating package with a dependency (rJava) that
> doesn't build on all flavours
> >
> > Hi,
> >
> > I maintain a package in CRAN, for which I am struggling to push the
> latest updates.
> >
> > The problem is as follows:
> > My package passes tests without error or notice on all flavors but one,
> where the install fails due to an installation error of a dependency
> package (package rJava on r-devel-windows-ix86+x86_64). This installation
> error was already there in the past submissions of my package to CRAN, and
> was not previously considered as a blocker to the package (or its updates)
> being accepted (Current CRAN status: ERROR: 1, OK: 10)
> >
> > Now, the package updates are automatically rejected:
> >
> > 
> >
> > package qCBA_0.4.tar.gz does not pass the incoming checks automatically,
> please see the following pre-tests:
> > Windows: <
> https://win-builder.r-project.org/incoming_pretest/qCBA_0.4_20191108_100822/Windows/00check.log
> >
> > Status: 1 ERROR
> > Debian: <
> https://win-builder.r-project.org/incoming_pretest/qCBA_0.4_20191108_100822/Debian/00check.log
> >
> > Status: OK
> >
> > 
> >
> > I cannot fix the problem with the dependency (rJava), and I als

[R-pkg-devel] warnings by 3rd party headers

2020-01-16 Thread Guido Kraemer
I need to distribute some 3rd party headers with my package. The headers 
make R CMD check produce warnings:


   File which contains pragma(s) suppressing important diagnostics:
   ...
   Files which contain pragma(s) suppressing diagnostics:
   ...

There are some additional NOTEs on the use of `std::cout` which is being 
used in some of the headers.


If I want to submit the package to CRAN in the future, do I have to edit 
the headers?


Cheers,

Guido

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Re: [R-pkg-devel] warnings by 3rd party headers

2020-01-16 Thread Iñaki Ucar
On Thu, 16 Jan 2020 at 16:58, Guido Kraemer  wrote:
>
> I need to distribute some 3rd party headers with my package. The headers
> make R CMD check produce warnings:
>
> File which contains pragma(s) suppressing important diagnostics:
> ...
> Files which contain pragma(s) suppressing diagnostics:
> ...
>
> There are some additional NOTEs on the use of `std::cout` which is being
> used in some of the headers.
>
> If I want to submit the package to CRAN in the future, do I have to edit
> the headers?

I think so. That's what, e.g., Dirk does for BH:
https://github.com/eddelbuettel/bh/commit/313da3cb04227d96daafa2d73668b30fa3fd10fc

Iñaki

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Re: [R-pkg-devel] warnings by 3rd party headers

2020-01-16 Thread Dirk Eddelbuettel


On 16 January 2020 at 17:06, Iñaki Ucar wrote:
| On Thu, 16 Jan 2020 at 16:58, Guido Kraemer  wrote:
| >
| > I need to distribute some 3rd party headers with my package. The headers
| > make R CMD check produce warnings:
| >
| > File which contains pragma(s) suppressing important diagnostics:
| > ...
| > Files which contain pragma(s) suppressing diagnostics:
| > ...
| >
| > There are some additional NOTEs on the use of `std::cout` which is being
| > used in some of the headers.
| >
| > If I want to submit the package to CRAN in the future, do I have to edit
| > the headers?
| 
| I think so. That's what, e.g., Dirk does for BH:
| 
https://github.com/eddelbuettel/bh/commit/313da3cb04227d96daafa2d73668b30fa3fd10fc

=:-)

Beat me to it. Was about to show the last diff:
https://github.com/eddelbuettel/bh/blob/master/local/patches/bh_1.72.0-0.diagnostics.patch

The policy is, if I may use salty language for once, idiotic^Ha really bad
call. But I don't get to make the policy so I just live by it.

So yes Guido, you have to.  And again on each upstream upgrade you cover.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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