Re: [R-pkg-devel] Troubleshooting Winbuilder Run Timeouts

[Andrew Robbins via R-package-devel]

I spent this afternoon trying to figure out what exactly was going on 
here. In my several submissions to winbuilder (sorry Uwe) I have 
confirmed that the culprit is /not/:


 * writing to Rcpp::rcout
 * openmp
 * std::chrono::high_resolution_clock

Every time, it reports a runtime of zero seconds for INMF res1 and 
hangs/is killed on initiation of INMF res2 before the initialization of 
RcppProgress. I'm at a bit of a loss here.



Best,

-Andrew


On 11/30/2023 9:30 AM, Andrew Robbins via R-package-devel wrote:

Hi Ivan,

Thank you for giving my package check a run-through. You have it 
correct-every win-builder log hangs/halts in that exact example. The 
only other anomaly I notice on win-builder is that the elapsed time 
reported to Rcout is 0-which is clearly incorrect. DNDEBUG removing 
the assert calls would certainly make my life quite a bit easier when 
it comes time to maintain the package, so I'll definitely give that a 
try. Re: declared requirements, WindowsOverrides contains slightly 
modified copies of cmake locator files with patches that will likely 
be included in a later Rtools43 release. I'm fairly sure pkgbuild in 
rtools can be assumed present, but that's more of a Tomas question 
(and it may be worth declaring either way). Regardless, those files 
aren't intended to stick around for any longer than they need to. Any 
other suggestions are always welcome, but I do get the feeling that 
something is fishy on win-builder's end.



Best,

Andrew

On 11/30/2023 7:40 AM, Ivan Krylov wrote:

Hi Andrew Robbins,

В Mon, 27 Nov 2023 12:22:44 -0500
Andrew Robbins via R-package-devel 
пишет:


I'm currently attempting to submit a package to CRAN and am getting
timeouts during the "running examples" phase of the winbuilder tests
that I cannot reproduce locally or on the r-hub windows runner

Do I understand it correctly that in multiple win-builder tests, you
always get a timeout in the same inmf example? Or is it different
examples?

There doesn't seem to be a lot of code between Rcpp::Rcerr << "INMF
started, niter=" << niter << std::endl; and Progress p(niter, verbose);
to crash or hang in. I've tried to reproduce the problem myself, but it
doesn't happen to me either.

So far I only noticed minor things, like the build-time dependency on
pkgbuild (from tools/WindowsOverrides/hdf5/hdf5-config.cmake) that may
be worth declaring in your DESCRIPTION. I also think that your patch to
hwloc can be reduced by adding a -DNDEBUG somewhere instead of patching
out calls to assert(). I think that the C standard (e.g. C99, WG14 draft
version N1256, 7.4) requires assert() to expand to ((void)0) if NDEBUG
is defined.

The amount of systems engineering effort to do the right thing that
went into this package is really impressive; I'd hate to see it fail.


__
R-package-devel@r-project.org  mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


--
Andrew Robbins
Systems Analyst, Welch Lab
University of Michigan
Department of Computational Medicine and Bioinformatics



OpenPGP_signature.asc
Description: OpenPGP digital signature
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Update timing of machines on CRAN?

[Andrew Robbins via R-package-devel]

I can't help with providing servers, but if the primary issue with 
builder software maintenance is manpower I would be more than willing to 
contribute and I imagine others would be as well. Perhaps logistically 
challenging, but more than doable.


-Andrew

On 12/4/2023 5:11 PM, Uwe Ligges wrote:
Thanks for your offer to providing us with capable multicore servers 
and support staff for continuing support of recent Fedora systems.


Best,
Uwe Ligges


On 04.12.2023 18:09, andrew--- via R-package-devel wrote:
I do think that its a reasonable ask that the test machines be 
running operating systems within their vendor support periods.


-Andrew Robbins

From: R-package-devel  on 
behalf of Josiah Parry 

Sent: Monday, December 4, 2023 11:34 AM
To: Tomas Kalibera 
Cc: R Package Development 
Subject: Re: [R-pkg-devel] Update timing of machines on CRAN?

Unfortunately, it is often important for us to pay attention to what
machines our code is being tested on.

I think the point is more or less that we often find ourselves trying to
make super small adjustments for machines and builds that are used by a
number of users in the single digits. The vast majority of R programmers
are not on these arcane machines. We should strive to support the vast
majority of users who use *fairly* standard distributions such as Mac,
Windows, Ubuntu, Debian, and maybe even Centos. Getting a note for a
release which has reach EOL can be confusing and tough to know how to
handle.

On Mon, Dec 4, 2023 at 10:17 AM Tomas Kalibera 


wrote:



On 12/4/23 15:44, SHIMA Tatsuya wrote:

Thanks for your answer.

Unlike Windows Server, which has a long support period, Fedora's
support period is usually about one year, so it is surprising that the
old Fedora continues to be used.
And, unlike Windows, Linux uses the distribution standard packages for
builds, which causes problems like the current Fedora machine that
continues to use the old Rust.


The configuration currently at different CRAN machines is just a sample
of what your users might have, just an example of a setting packages
should be able to deal with. Some users might also still have FC36, 
some

might have another Linux distribution (possibly still supported), which
has older software than that.

I wouldn't recommend spending time tracking which version of which
software CRAN systems currently happen to have, but rather making sure
packages can deal with different versions (possibly with some in a
restricted way, possibly making some hard requirements when necessary).

Best
Tomas


Hope to see an update soon. Thanks to the staff for maintaining the
infrastructure.

Best,
Tatsuya

On 2023/12/01 23:43, Uwe Ligges wrote:



On 01.12.2023 13:28, SHIMA Tatsuya wrote:

Hi,

I maintain the prqlr package that uses rustc for compiling, so I
regularly check the version of Rust on CRAN.
And I have noticed that the Rust version of Fedora has been stagnant
for the past few months and was wondering why, but upon
investigation I realized that this is because Fedora on CRAN is
currently Fedora 36 (out of support in May).


It was quite a surprise to me that out of support Fedora is being
used, but what is the normal cycle for machines on CRAN to be
updated? And do we have any way of knowing that schedule?


It depends on the maintainer who cares about these machine, the
institution where it is hosted, the availability of technical staff,
and the technical pressure.

I could not even say when the machines I maintain will be updated.
On one version of the retired winbuilder severs we kept the same OS
version for almost 10 years.

Best,
Uwe Ligges







Best,
Tatsuya

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel



 [[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[[alternative HTML version deleted]]

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


--
Andrew Robbins
Systems Analyst, Welch Lab
University of Michigan
Department of Computational Medicine and Bioinformatics



OpenPGP_signature.asc
Description: OpenPGP digital signature
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] macos x86 oldrel backups?

[Dirk Eddelbuettel]

Hi Simon,

On 5 December 2023 at 23:17, Simon Urbanek wrote:
| The high-sierra build packages are currently not built due to hardware 
issues. The macOS version is so long out of support by Apple (over 6 years) 
that it is hard to maintain it. Only big-sur builds are supported at this 
point. Although it is possible that we may be able to restore the old builds, 
it is not guaranteed. (BTW the right mailing list for this is R-SIG-Mac).

Interesting.  And I see at mac.r-project.org the statement

   [...] As of R 4.3.0 we maintain two binary builds:

   - big-sur-x86_64 build supports legacy Intel Macs from macOS 11 (Big Sur) 
and higher
   - big-sur-arm64 build supports arm64 Macs (M1+) from macOS 11 (Big Sur) and 
higher

   We are no longer building binaries for macOS versions before 11 (as they
   are no longer supported by Apple).

so it is official that r-oldrel on macOS is no more for now? So we do not
have to worry about compilation standards lower than 11.0?  Do I have that
correct? 

Dirk
not on r-sig-mac, appreciative of any hints here as that is what we created the 
list for
 
| Cheers,
| Simon
| 
| 
| 
| > On 5/12/2023, at 09:52, Jonathan Keane  wrote:
| > 
| > Thank you to the CRAN maintainers for maintenance and keeping the all
| > of the CRAN infrastructure running.
| > 
| > I'm seeing a long delay in builds on CRAN for r-oldrel-macos-x86_64.
| > I'm currently interested in Arrow [1], but I'm seeing many other
| > packages with similar missing r-oldrel-macos-x86_64 builds (possibly
| > all, I sampled a few packages from [2], but didn't do an exhaustive
| > search) for an extended period.
| > 
| > It appears that this started between 2023-10-21 and 2023-10-22. It
| > looks like AMR [3] has a successful build but xlcutter does not [4]
| > and all the packages I've checked after 2023-10-22 don't have an
| > updated build for r-oldrel-macos-x86_64
| > 
| > Sorry if this is scheduled maintenance, I tried to find an
| > announcement here and on r-project.org but haven't yet found anything
| > indicating this.
| > 
| > [1] - https://cran.r-project.org/web/checks/check_results_arrow.html
| > [2] - 
https://cran.r-project.org/web/packages/available_packages_by_date.html
| > [3] - https://cran.r-project.org/web/packages/AMR/index.html
| > [4] - https://cran.r-project.org/web/packages/xlcutter/index.html
| > 
| > -Jon
| > 
| > __
| > R-package-devel@r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-package-devel
| > 
| 
| __
| R-package-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-package-devel

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] macos x86 oldrel backups?

[Simon Urbanek]

Jon,

The high-sierra build packages are currently not built due to hardware issues. 
The macOS version is so long out of support by Apple (over 6 years) that it is 
hard to maintain it. Only big-sur builds are supported at this point. Although 
it is possible that we may be able to restore the old builds, it is not 
guaranteed. (BTW the right mailing list for this is R-SIG-Mac).

Cheers,
Simon



> On 5/12/2023, at 09:52, Jonathan Keane  wrote:
> 
> Thank you to the CRAN maintainers for maintenance and keeping the all
> of the CRAN infrastructure running.
> 
> I'm seeing a long delay in builds on CRAN for r-oldrel-macos-x86_64.
> I'm currently interested in Arrow [1], but I'm seeing many other
> packages with similar missing r-oldrel-macos-x86_64 builds (possibly
> all, I sampled a few packages from [2], but didn't do an exhaustive
> search) for an extended period.
> 
> It appears that this started between 2023-10-21 and 2023-10-22. It
> looks like AMR [3] has a successful build but xlcutter does not [4]
> and all the packages I've checked after 2023-10-22 don't have an
> updated build for r-oldrel-macos-x86_64
> 
> Sorry if this is scheduled maintenance, I tried to find an
> announcement here and on r-project.org but haven't yet found anything
> indicating this.
> 
> [1] - https://cran.r-project.org/web/checks/check_results_arrow.html
> [2] - https://cran.r-project.org/web/packages/available_packages_by_date.html
> [3] - https://cran.r-project.org/web/packages/AMR/index.html
> [4] - https://cran.r-project.org/web/packages/xlcutter/index.html
> 
> -Jon
> 
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> 

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] macos x86 oldrel backups?

[Uwe Ligges]

Have you sent a note to the Mac maintainer already?

Best,
Uwe Ligges



On 04.12.2023 21:52, Jonathan Keane wrote:

Thank you to the CRAN maintainers for maintenance and keeping the all
of the CRAN infrastructure running.

I'm seeing a long delay in builds on CRAN for r-oldrel-macos-x86_64.
I'm currently interested in Arrow [1], but I'm seeing many other
packages with similar missing r-oldrel-macos-x86_64 builds (possibly
all, I sampled a few packages from [2], but didn't do an exhaustive
search) for an extended period.

It appears that this started between 2023-10-21 and 2023-10-22. It
looks like AMR [3] has a successful build but xlcutter does not [4]
and all the packages I've checked after 2023-10-22 don't have an
updated build for r-oldrel-macos-x86_64

Sorry if this is scheduled maintenance, I tried to find an
announcement here and on r-project.org but haven't yet found anything
indicating this.

[1] - https://cran.r-project.org/web/checks/check_results_arrow.html
[2] - https://cran.r-project.org/web/packages/available_packages_by_date.html
[3] - https://cran.r-project.org/web/packages/AMR/index.html
[4] - https://cran.r-project.org/web/packages/xlcutter/index.html

-Jon

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel


__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] macos x86 oldrel backups?

[Jonathan Keane]

Thank you to the CRAN maintainers for maintenance and keeping the all
of the CRAN infrastructure running.

I'm seeing a long delay in builds on CRAN for r-oldrel-macos-x86_64.
I'm currently interested in Arrow [1], but I'm seeing many other
packages with similar missing r-oldrel-macos-x86_64 builds (possibly
all, I sampled a few packages from [2], but didn't do an exhaustive
search) for an extended period.

It appears that this started between 2023-10-21 and 2023-10-22. It
looks like AMR [3] has a successful build but xlcutter does not [4]
and all the packages I've checked after 2023-10-22 don't have an
updated build for r-oldrel-macos-x86_64

Sorry if this is scheduled maintenance, I tried to find an
announcement here and on r-project.org but haven't yet found anything
indicating this.

[1] - https://cran.r-project.org/web/checks/check_results_arrow.html
[2] - https://cran.r-project.org/web/packages/available_packages_by_date.html
[3] - https://cran.r-project.org/web/packages/AMR/index.html
[4] - https://cran.r-project.org/web/packages/xlcutter/index.html

-Jon

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel