R 3.6.1

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R 3.6.1

Jan Galkowski-2
Did something seriously change in R 3.6.1 at least for Windows in terms of stack impacts?

I'm encountering many problems with the 00UNLOCK, needing to disable locking during installations.

And I'm encountering

> Error: C stack usage 63737888 is too close to the limit

for cases I did not before, even when all I'm doing is serializing an object to be saved with *saveRDS* or even *save.image(.)*.

Yes, I know, I did not append a minimally complete example. Just wanted to see if it was just me, or if anyone else was seeing this.

It's on Windows 7 HE and I've run *R* here for years.

My inclination is to drop back to 3.6.0 if it is just me or if no one knows about this problem.

Thanks,

 - Jan Galkowski.


        [[alternative HTML version deleted]]

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Re: R 3.6.1

Jeff Newmiller
It would never make sense for such messages to reflect normal and expected operation, so hypothesizing about intentionally changing stack behavior doesn't make sense.

The default format for saveRDS changed in 3.6.0. There may be bugs associated with that, but rolling back to 3.6.0 would just trade bugs.

https://cran.r-project.org/doc/manuals/r-devel/NEWS.html

On July 16, 2019 8:56:28 PM CDT, Jan Galkowski <[hidden email]> wrote:

>Did something seriously change in R 3.6.1 at least for Windows in terms
>of stack impacts?
>
>I'm encountering many problems with the 00UNLOCK, needing to disable
>locking during installations.
>
>And I'm encountering
>
>> Error: C stack usage 63737888 is too close to the limit
>
>for cases I did not before, even when all I'm doing is serializing an
>object to be saved with *saveRDS* or even *save.image(.)*.
>
>Yes, I know, I did not append a minimally complete example. Just wanted
>to see if it was just me, or if anyone else was seeing this.
>
>It's on Windows 7 HE and I've run *R* here for years.
>
>My inclination is to drop back to 3.6.0 if it is just me or if no one
>knows about this problem.
>
>Thanks,
>
> - Jan Galkowski.
>
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: R 3.6.1

Spencer Graves-4
       What might be the likely outcomes of an attempt to reinstall 3.6.1?


       And might that depend on whether the current 3.6.1 was
uninstalled first?


       Spencer


On 2019-07-17 07:17, Jeff Newmiller wrote:

> It would never make sense for such messages to reflect normal and
> expected operation, so hypothesizing about intentionally changing
> stack behavior doesn't make sense.
>
> The default format for saveRDS changed in 3.6.0. There may be bugs
> associated with that, but rolling back to 3.6.0 would just trade bugs.
>
> https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>
> On July 16, 2019 8:56:28 PM CDT, Jan Galkowski
> <[hidden email]> wrote:
>> Did something seriously change in R 3.6.1 at least for Windows in terms
>> of stack impacts?
>>
>> I'm encountering many problems with the 00UNLOCK, needing to disable
>> locking during installations.
>>
>> And I'm encountering
>>
>>> Error: C stack usage 63737888 is too close to the limit
>> for cases I did not before, even when all I'm doing is serializing an
>> object to be saved with *saveRDS* or even *save.image(.)*.
>>
>> Yes, I know, I did not append a minimally complete example. Just wanted
>> to see if it was just me, or if anyone else was seeing this.
>>
>> It's on Windows 7 HE and I've run *R* here for years.
>>
>> My inclination is to drop back to 3.6.0 if it is just me or if no one
>> knows about this problem.
>>
>> Thanks,
>>
>> - Jan Galkowski.
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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Re: R 3.6.1

Jeff Newmiller
I think that would depend on whether the bug was in the install program or not. In this case I would not bet on that being the problem.

I would either look for a patched release that addresses the bug, or roll back to 3.5.3. You might have luck with 3.6.0, but given that was when the major feature update occurred that option seems risky to me.

On July 17, 2019 8:13:53 AM CDT, Spencer Graves <[hidden email]> wrote:

>      What might be the likely outcomes of an attempt to reinstall
>3.6.1?
>
>
>       And might that depend on whether the current 3.6.1 was
>uninstalled first?
>
>
>       Spencer
>
>
>On 2019-07-17 07:17, Jeff Newmiller wrote:
>> It would never make sense for such messages to reflect normal and
>> expected operation, so hypothesizing about intentionally changing
>> stack behavior doesn't make sense.
>>
>> The default format for saveRDS changed in 3.6.0. There may be bugs
>> associated with that, but rolling back to 3.6.0 would just trade
>bugs.
>>
>> https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>>
>> On July 16, 2019 8:56:28 PM CDT, Jan Galkowski
>> <[hidden email]> wrote:
>>> Did something seriously change in R 3.6.1 at least for Windows in
>terms
>>> of stack impacts?
>>>
>>> I'm encountering many problems with the 00UNLOCK, needing to disable
>>> locking during installations.
>>>
>>> And I'm encountering
>>>
>>>> Error: C stack usage 63737888 is too close to the limit
>>> for cases I did not before, even when all I'm doing is serializing
>an
>>> object to be saved with *saveRDS* or even *save.image(.)*.
>>>
>>> Yes, I know, I did not append a minimally complete example. Just
>wanted
>>> to see if it was just me, or if anyone else was seeing this.
>>>
>>> It's on Windows 7 HE and I've run *R* here for years.
>>>
>>> My inclination is to drop back to 3.6.0 if it is just me or if no
>one
>>> knows about this problem.
>>>
>>> Thanks,
>>>
>>> - Jan Galkowski.
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>
>______________________________________________
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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R 3.6.1 and apcluster package

Jan Galkowski-2
In reply to this post by Jeff Newmiller
> # Test for saving. Jan Galkowski, 17th July 2019.
> # produceProtectionFault.R
>
> library(apcluster)
> cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
> cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
> x <- rbind(cl1, cl2)
>
> ## compute similarity matrix and run affinity propagation
> ## (p defaults to median of similarity)
> simil<- negDistMat(x, r=2)
> apres <- apcluster(s=simil, details=TRUE)
> apresX<- aggExCluster(s=simil, x=apres)
>
> show(apres)
> show(apresX)
>
> saveRDS(object=apresX, file="foo.rds", compress=TRUE)
>
> #save(apresX, file="bar.data", compress=TRUE)
>
> #save.image("crazy.RData")

The example is from the apcluster documentation. Leaving any one of the "save"s uncommented produces said fault.

 - Jan

On Wed, Jul 17, 2019, at 08:18, Jeff Newmiller wrote:

> It would never make sense for such messages to reflect normal and expected operation, so hypothesizing about intentionally changing stack behavior doesn't make sense.
>
> The default format for saveRDS changed in 3.6.0. There may be bugs associated with that, but rolling back to 3.6.0 would just trade bugs.
>
> https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>
> On July 16, 2019 8:56:28 PM CDT, Jan Galkowski <[hidden email]> wrote:
> >Did something seriously change in R 3.6.1 at least for Windows in terms
> >of stack impacts?
> >
> >I'm encountering many problems with the 00UNLOCK, needing to disable
> >locking during installations.
> >
> >And I'm encountering
> >
> >> Error: C stack usage 63737888 is too close to the limit
> >
> >for cases I did not before, even when all I'm doing is serializing an
> >object to be saved with *saveRDS* or even *save.image(.)*.
> >
> >Yes, I know, I did not append a minimally complete example. Just wanted
> >to see if it was just me, or if anyone else was seeing this.
> >
> >It's on Windows 7 HE and I've run *R* here for years.
> >
> >My inclination is to drop back to 3.6.0 if it is just me or if no one
> >knows about this problem.
> >
> >Thanks,
> >
> > - Jan Galkowski.
> >
> >
> > [[alternative HTML version deleted]]
> >
> >______________________________________________
> >[hidden email] mailing list -- To UNSUBSCRIBE and more, see
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
> --
> Sent from my phone. Please excuse my brevity.
>

--
Jan Galkowski (o°)

607.239.1834 [mobile]
607.239.1834 [home]

[hidden email]
http://667-per-cm.net

member,

... American Statistical Association
... International Society for Bayesian Analysis
... Ecological Society of America
... International Association of Survey Statisticians
... American Association for the Advancement of Science
... TeX Users Group

(pronouns: *he, him, his*)

*Keep your energy local*. --John Farrell, *ILSR <http://ilsr.org/>*


        [[alternative HTML version deleted]]

______________________________________________
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Re: R 3.6.1

Martin Maechler
In reply to this post by Jan Galkowski-2
>>>>> "JG" == Jan Galkowski
>>>>>     on Tue, 16 Jul 2019 21:56:28 -0400 writes:

    JG> Did something seriously change in R 3.6.1 at least for Windows in terms of stack impacts?
    JG> I'm encountering many problems with the 00UNLOCK, needing to disable locking during installations.

    JG> And I'm encountering

    >> Error: C stack usage 63737888 is too close to the limit

    JG> for cases I did not before, even when all I'm doing is serializing an object to be saved with *saveRDS* or even *save.image(.)*.

    JG> Yes, I know, I did not append a minimally complete example. Just wanted to see if it was just me, or if anyone else was seeing this.

    JG> It's on Windows 7 HE and I've run *R* here for years.

    JG> My inclination is to drop back to 3.6.0 if it is just me or if no one knows about this problem.

The last sentence suggests, you did have 3.6.0 installed and you
are sure to not have seen such problems ??

In that case even more, we (R core, notably) would be interested
to see a minimal repr.ex  triggering the problem.
(and what is  '00UNLOCK' ?)

    JG> Thanks,

    JG> - Jan Galkowski.

Best
Martin Maechler


    JG> [[alternative HTML version deleted]]
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  Please chose 'plain text' (Gmail: easily possible)

    JG> ______________________________________________
    JG> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    JG> https://stat.ethz.ch/mailman/listinfo/r-help
    JG> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    JG> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: R 3.6.1 and apcluster package

R help mailing list-2
In reply to this post by Jan Galkowski-2
Note that you can reproduce this in R-3.5.1 if you specify serialization
version 3 (which became the default in 3.6.0).

> save(apresX, file="351-2.RData", version=2)
> save(apresX, file="351-2.RData", version=3)
Error: C stack usage  7969184 is too close to the limit
> version$version.string
[1] "R version 3.5.1 (2018-07-02)"

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Thu, Jul 18, 2019 at 12:46 AM Jan Galkowski <[hidden email]>
wrote:

> > # Test for saving. Jan Galkowski, 17th July 2019.
> > # produceProtectionFault.R
> >
> > library(apcluster)
> > cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
> > cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
> > x <- rbind(cl1, cl2)
> >
> > ## compute similarity matrix and run affinity propagation
> > ## (p defaults to median of similarity)
> > simil<- negDistMat(x, r=2)
> > apres <- apcluster(s=simil, details=TRUE)
> > apresX<- aggExCluster(s=simil, x=apres)
> >
> > show(apres)
> > show(apresX)
> >
> > saveRDS(object=apresX, file="foo.rds", compress=TRUE)
> >
> > #save(apresX, file="bar.data", compress=TRUE)
> >
> > #save.image("crazy.RData")
>
> The example is from the apcluster documentation. Leaving any one of the
> "save"s uncommented produces said fault.
>
>  - Jan
>
> On Wed, Jul 17, 2019, at 08:18, Jeff Newmiller wrote:
> > It would never make sense for such messages to reflect normal and
> expected operation, so hypothesizing about intentionally changing stack
> behavior doesn't make sense.
> >
> > The default format for saveRDS changed in 3.6.0. There may be bugs
> associated with that, but rolling back to 3.6.0 would just trade bugs.
> >
> > https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
> >
> > On July 16, 2019 8:56:28 PM CDT, Jan Galkowski <
> [hidden email]> wrote:
> > >Did something seriously change in R 3.6.1 at least for Windows in terms
> > >of stack impacts?
> > >
> > >I'm encountering many problems with the 00UNLOCK, needing to disable
> > >locking during installations.
> > >
> > >And I'm encountering
> > >
> > >> Error: C stack usage 63737888 is too close to the limit
> > >
> > >for cases I did not before, even when all I'm doing is serializing an
> > >object to be saved with *saveRDS* or even *save.image(.)*.
> > >
> > >Yes, I know, I did not append a minimally complete example. Just wanted
> > >to see if it was just me, or if anyone else was seeing this.
> > >
> > >It's on Windows 7 HE and I've run *R* here for years.
> > >
> > >My inclination is to drop back to 3.6.0 if it is just me or if no one
> > >knows about this problem.
> > >
> > >Thanks,
> > >
> > > - Jan Galkowski.
> > >
> > >
> > > [[alternative HTML version deleted]]
> > >
> > >______________________________________________
> > >[hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > >https://stat.ethz.ch/mailman/listinfo/r-help
> > >PLEASE do read the posting guide
> > >http://www.R-project.org/posting-guide.html
> > >and provide commented, minimal, self-contained, reproducible code.
> >
> > --
> > Sent from my phone. Please excuse my brevity.
> >
>
> --
> Jan Galkowski (o°)
>
> 607.239.1834 [mobile]
> 607.239.1834 [home]
>
> [hidden email]
> http://667-per-cm.net
>
> member,
>
> ... American Statistical Association
> ... International Society for Bayesian Analysis
> ... Ecological Society of America
> ... International Association of Survey Statisticians
> ... American Association for the Advancement of Science
> ... TeX Users Group
>
> (pronouns: *he, him, his*)
>
> *Keep your energy local*. --John Farrell, *ILSR <http://ilsr.org/>*
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: R 3.6.1 and apcluster package

R help mailing list-2
If you use version=3, ascii=TRUE and look at the file made up to the point
of the error, you can see a quasi-infinite repeat of a block of 165 numbers
(after a deferred string called "base"?).  Looks like inappropriate
recursion.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Thu, Jul 18, 2019 at 7:38 AM William Dunlap <[hidden email]> wrote:

> Note that you can reproduce this in R-3.5.1 if you specify serialization
> version 3 (which became the default in 3.6.0).
>
> > save(apresX, file="351-2.RData", version=2)
> > save(apresX, file="351-2.RData", version=3)
> Error: C stack usage  7969184 is too close to the limit
> > version$version.string
> [1] "R version 3.5.1 (2018-07-02)"
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Thu, Jul 18, 2019 at 12:46 AM Jan Galkowski <[hidden email]>
> wrote:
>
>> > # Test for saving. Jan Galkowski, 17th July 2019.
>> > # produceProtectionFault.R
>> >
>> > library(apcluster)
>> > cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
>> > cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
>> > x <- rbind(cl1, cl2)
>> >
>> > ## compute similarity matrix and run affinity propagation
>> > ## (p defaults to median of similarity)
>> > simil<- negDistMat(x, r=2)
>> > apres <- apcluster(s=simil, details=TRUE)
>> > apresX<- aggExCluster(s=simil, x=apres)
>> >
>> > show(apres)
>> > show(apresX)
>> >
>> > saveRDS(object=apresX, file="foo.rds", compress=TRUE)
>> >
>> > #save(apresX, file="bar.data", compress=TRUE)
>> >
>> > #save.image("crazy.RData")
>>
>> The example is from the apcluster documentation. Leaving any one of the
>> "save"s uncommented produces said fault.
>>
>>  - Jan
>>
>> On Wed, Jul 17, 2019, at 08:18, Jeff Newmiller wrote:
>> > It would never make sense for such messages to reflect normal and
>> expected operation, so hypothesizing about intentionally changing stack
>> behavior doesn't make sense.
>> >
>> > The default format for saveRDS changed in 3.6.0. There may be bugs
>> associated with that, but rolling back to 3.6.0 would just trade bugs.
>> >
>> > https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>> >
>> > On July 16, 2019 8:56:28 PM CDT, Jan Galkowski <
>> [hidden email]> wrote:
>> > >Did something seriously change in R 3.6.1 at least for Windows in terms
>> > >of stack impacts?
>> > >
>> > >I'm encountering many problems with the 00UNLOCK, needing to disable
>> > >locking during installations.
>> > >
>> > >And I'm encountering
>> > >
>> > >> Error: C stack usage 63737888 is too close to the limit
>> > >
>> > >for cases I did not before, even when all I'm doing is serializing an
>> > >object to be saved with *saveRDS* or even *save.image(.)*.
>> > >
>> > >Yes, I know, I did not append a minimally complete example. Just wanted
>> > >to see if it was just me, or if anyone else was seeing this.
>> > >
>> > >It's on Windows 7 HE and I've run *R* here for years.
>> > >
>> > >My inclination is to drop back to 3.6.0 if it is just me or if no one
>> > >knows about this problem.
>> > >
>> > >Thanks,
>> > >
>> > > - Jan Galkowski.
>> > >
>> > >
>> > > [[alternative HTML version deleted]]
>> > >
>> > >______________________________________________
>> > >[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> > >https://stat.ethz.ch/mailman/listinfo/r-help
>> > >PLEASE do read the posting guide
>> > >http://www.R-project.org/posting-guide.html
>> > >and provide commented, minimal, self-contained, reproducible code.
>> >
>> > --
>> > Sent from my phone. Please excuse my brevity.
>> >
>>
>> --
>> Jan Galkowski (o°)
>>
>> 607.239.1834 [mobile]
>> 607.239.1834 [home]
>>
>> [hidden email]
>> http://667-per-cm.net
>>
>> member,
>>
>> ... American Statistical Association
>> ... International Society for Bayesian Analysis
>> ... Ecological Society of America
>> ... International Association of Survey Statisticians
>> ... American Association for the Advancement of Science
>> ... TeX Users Group
>>
>> (pronouns: *he, him, his*)
>>
>> *Keep your energy local*. --John Farrell, *ILSR <http://ilsr.org/>*
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [External] Re: R 3.6.1 and apcluster package

Tierney, Luke
Something about the deferred string conversion object in

a <- names(attributes(apresX)[[4]][[1]][[1]])

is malformed; .Internal(inspect(a)) also infinite loops.
Will try to narrow this down.

Best,

luke

On Thu, 18 Jul 2019, William Dunlap via R-help wrote:

> If you use version=3, ascii=TRUE and look at the file made up to the point
> of the error, you can see a quasi-infinite repeat of a block of 165 numbers
> (after a deferred string called "base"?).  Looks like inappropriate
> recursion.
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Thu, Jul 18, 2019 at 7:38 AM William Dunlap <[hidden email]> wrote:
>
>> Note that you can reproduce this in R-3.5.1 if you specify serialization
>> version 3 (which became the default in 3.6.0).
>>
>>> save(apresX, file="351-2.RData", version=2)
>>> save(apresX, file="351-2.RData", version=3)
>> Error: C stack usage  7969184 is too close to the limit
>>> version$version.string
>> [1] "R version 3.5.1 (2018-07-02)"
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>>
>> On Thu, Jul 18, 2019 at 12:46 AM Jan Galkowski <[hidden email]>
>> wrote:
>>
>>>> # Test for saving. Jan Galkowski, 17th July 2019.
>>>> # produceProtectionFault.R
>>>>
>>>> library(apcluster)
>>>> cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
>>>> cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
>>>> x <- rbind(cl1, cl2)
>>>>
>>>> ## compute similarity matrix and run affinity propagation
>>>> ## (p defaults to median of similarity)
>>>> simil<- negDistMat(x, r=2)
>>>> apres <- apcluster(s=simil, details=TRUE)
>>>> apresX<- aggExCluster(s=simil, x=apres)
>>>>
>>>> show(apres)
>>>> show(apresX)
>>>>
>>>> saveRDS(object=apresX, file="foo.rds", compress=TRUE)
>>>>
>>>> #save(apresX, file="bar.data", compress=TRUE)
>>>>
>>>> #save.image("crazy.RData")
>>>
>>> The example is from the apcluster documentation. Leaving any one of the
>>> "save"s uncommented produces said fault.
>>>
>>>  - Jan
>>>
>>> On Wed, Jul 17, 2019, at 08:18, Jeff Newmiller wrote:
>>>> It would never make sense for such messages to reflect normal and
>>> expected operation, so hypothesizing about intentionally changing stack
>>> behavior doesn't make sense.
>>>>
>>>> The default format for saveRDS changed in 3.6.0. There may be bugs
>>> associated with that, but rolling back to 3.6.0 would just trade bugs.
>>>>
>>>> https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>>>>
>>>> On July 16, 2019 8:56:28 PM CDT, Jan Galkowski <
>>> [hidden email]> wrote:
>>>>> Did something seriously change in R 3.6.1 at least for Windows in terms
>>>>> of stack impacts?
>>>>>
>>>>> I'm encountering many problems with the 00UNLOCK, needing to disable
>>>>> locking during installations.
>>>>>
>>>>> And I'm encountering
>>>>>
>>>>>> Error: C stack usage 63737888 is too close to the limit
>>>>>
>>>>> for cases I did not before, even when all I'm doing is serializing an
>>>>> object to be saved with *saveRDS* or even *save.image(.)*.
>>>>>
>>>>> Yes, I know, I did not append a minimally complete example. Just wanted
>>>>> to see if it was just me, or if anyone else was seeing this.
>>>>>
>>>>> It's on Windows 7 HE and I've run *R* here for years.
>>>>>
>>>>> My inclination is to drop back to 3.6.0 if it is just me or if no one
>>>>> knows about this problem.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> - Jan Galkowski.
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>> --
>>>> Sent from my phone. Please excuse my brevity.
>>>>
>>>
>>> --
>>> Jan Galkowski (o°)
>>>
>>> 607.239.1834 [mobile]
>>> 607.239.1834 [home]
>>>
>>> [hidden email]
>>> http://667-per-cm.net
>>>
>>> member,
>>>
>>> ... American Statistical Association
>>> ... International Society for Bayesian Analysis
>>> ... Ecological Society of America
>>> ... International Association of Survey Statisticians
>>> ... American Association for the Advancement of Science
>>> ... TeX Users Group
>>>
>>> (pronouns: *he, him, his*)
>>>
>>> *Keep your energy local*. --John Farrell, *ILSR <http://ilsr.org/>*
>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   [hidden email]
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: R 3.6.1 and apcluster package

Jan Galkowski-2
In reply to this post by R help mailing list-2
I have confirmed that a complete workaround to these problems is available if, as Bill Dunlap suggested, "version=2" is used in all *save* incantations.

Thanks Bill!

 - Jan

On Thu, Jul 18, 2019, at 10:39, William Dunlap wrote:

> Note that you can reproduce this in R-3.5.1 if you specify serialization version 3 (which became the default in 3.6.0).
>
> > save(apresX, file="351-2.RData", version=2)
> > save(apresX, file="351-2.RData", version=3)
> Error: C stack usage 7969184 is too close to the limit
> > version$version.string
> [1] "R version 3.5.1 (2018-07-02)"
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Thu, Jul 18, 2019 at 12:46 AM Jan Galkowski <[hidden email]> wrote:
>> > # Test for saving. Jan Galkowski, 17th July 2019.
>>  > # produceProtectionFault.R
>>  >
>>  > library(apcluster)
>>  > cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
>>  > cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
>>  > x <- rbind(cl1, cl2)
>>  >
>>  > ## compute similarity matrix and run affinity propagation
>>  > ## (p defaults to median of similarity)
>>  > simil<- negDistMat(x, r=2)
>>  > apres <- apcluster(s=simil, details=TRUE)
>>  > apresX<- aggExCluster(s=simil, x=apres)
>>  >
>>  > show(apres)
>>  > show(apresX)
>>  >
>>  > saveRDS(object=apresX, file="foo.rds", compress=TRUE)
>>  >
>>  > #save(apresX, file="bar.data", compress=TRUE)
>>  >
>>  > #save.image("crazy.RData")
>>
>>  The example is from the apcluster documentation. Leaving any one of the "save"s uncommented produces said fault.
>>
>>  - Jan
>>
>>  On Wed, Jul 17, 2019, at 08:18, Jeff Newmiller wrote:
>>  > It would never make sense for such messages to reflect normal and expected operation, so hypothesizing about intentionally changing stack behavior doesn't make sense.
>>  >
>>  > The default format for saveRDS changed in 3.6.0. There may be bugs associated with that, but rolling back to 3.6.0 would just trade bugs.
>>  >
>>  > https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>>  >
>>  > On July 16, 2019 8:56:28 PM CDT, Jan Galkowski <[hidden email]> wrote:
>>  > >Did something seriously change in R 3.6.1 at least for Windows in terms
>>  > >of stack impacts?
>>  > >
>>  > >I'm encountering many problems with the 00UNLOCK, needing to disable
>>  > >locking during installations.
>>  > >
>>  > >And I'm encountering
>>  > >
>>  > >> Error: C stack usage 63737888 is too close to the limit
>>  > >
>>  > >for cases I did not before, even when all I'm doing is serializing an
>>  > >object to be saved with *saveRDS* or even *save.image(.)*.
>>  > >
>>  > >Yes, I know, I did not append a minimally complete example. Just wanted
>>  > >to see if it was just me, or if anyone else was seeing this.
>>  > >
>>  > >It's on Windows 7 HE and I've run *R* here for years.
>>  > >
>>  > >My inclination is to drop back to 3.6.0 if it is just me or if no one
>>  > >knows about this problem.
>>  > >
>>  > >Thanks,
>>  > >
>>  > > - Jan Galkowski.
>>  [snip]

        [[alternative HTML version deleted]]

______________________________________________
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Re: [External] Re: R 3.6.1 and apcluster package

Tierney, Luke
On Thu, 18 Jul 2019, Jan Galkowski wrote:

> I have confirmed that a complete workaround to these problems is available if, as Bill Dunlap suggested, "version=2" is used in all *save* incantations.

That will mask this particular symptom, but the real problem is that
the C++ code in the package is mutating an object that it should
duplicate first. I'm not sure if the problem should be addressed in
the package or in Rcpp, but one of the two should be fixed.

The specific problem is in the source file
apcluster/src/aggExClusterC.cpp lines 160-161:

         IntegerVector newClust = concat(actClust[I], actClust[J]);
         newClust.names() = CharacterVector(newClust);

The call CharacterVector(newClust) produced a deferred string object
for newClust and marks newClust as immutable, but the assignment
ignores that and mutates anyway. I have CC'd the maintainers of
apcluster and Rcpp.

We may be able to make serialize() and .Internal(inspect()) a bit more
robust to this sort of misbehavior in package space, but as more
optimizations are added package authors who use native code will need
to be more careful about adhering to the rules for when objects can be
safely modified.

Best,

luke

> Thanks Bill!
>
> - Jan
>
> On Thu, Jul 18, 2019, at 10:39, William Dunlap wrote:
>> Note that you can reproduce this in R-3.5.1 if you specify serialization version 3 (which became the default in 3.6.0).
>>
>>> save(apresX, file="351-2.RData", version=2)
>>> save(apresX, file="351-2.RData", version=3)
>> Error: C stack usage 7969184 is too close to the limit
>>> version$version.string
>> [1] "R version 3.5.1 (2018-07-02)"
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>>
>> On Thu, Jul 18, 2019 at 12:46 AM Jan Galkowski <[hidden email]> wrote:
>>>> # Test for saving. Jan Galkowski, 17th July 2019.
>>> > # produceProtectionFault.R
>>> >
>>> > library(apcluster)
>>> > cl1 <- cbind(rnorm(100, 0.2, 0.05), rnorm(100, 0.8, 0.06))
>>> > cl2 <- cbind(rnorm(50, 0.7, 0.08), rnorm(50, 0.3, 0.05))
>>> > x <- rbind(cl1, cl2)
>>> >
>>> > ## compute similarity matrix and run affinity propagation
>>> > ## (p defaults to median of similarity)
>>> > simil<- negDistMat(x, r=2)
>>> > apres <- apcluster(s=simil, details=TRUE)
>>> > apresX<- aggExCluster(s=simil, x=apres)
>>> >
>>> > show(apres)
>>> > show(apresX)
>>> >
>>> > saveRDS(object=apresX, file="foo.rds", compress=TRUE)
>>> >
>>> > #save(apresX, file="bar.data", compress=TRUE)
>>> >
>>> > #save.image("crazy.RData")
>>>
>>>  The example is from the apcluster documentation. Leaving any one of the "save"s uncommented produces said fault.
>>>
>>>  - Jan
>>>
>>>  On Wed, Jul 17, 2019, at 08:18, Jeff Newmiller wrote:
>>> > It would never make sense for such messages to reflect normal and expected operation, so hypothesizing about intentionally changing stack behavior doesn't make sense.
>>> >
>>> > The default format for saveRDS changed in 3.6.0. There may be bugs associated with that, but rolling back to 3.6.0 would just trade bugs.
>>> >
>>> > https://cran.r-project.org/doc/manuals/r-devel/NEWS.html
>>> >
>>> > On July 16, 2019 8:56:28 PM CDT, Jan Galkowski <[hidden email]> wrote:
>>> >>Did something seriously change in R 3.6.1 at least for Windows in terms
>>> >>of stack impacts?
>>> >>
>>> >>I'm encountering many problems with the 00UNLOCK, needing to disable
>>> >>locking during installations.
>>> >>
>>> >>And I'm encountering
>>> >>
>>> >>> Error: C stack usage 63737888 is too close to the limit
>>> >>
>>> >>for cases I did not before, even when all I'm doing is serializing an
>>> >>object to be saved with *saveRDS* or even *save.image(.)*.
>>> >>
>>> >>Yes, I know, I did not append a minimally complete example. Just wanted
>>> >>to see if it was just me, or if anyone else was seeing this.
>>> >>
>>> >>It's on Windows 7 HE and I've run *R* here for years.
>>> >>
>>> >>My inclination is to drop back to 3.6.0 if it is just me or if no one
>>> >>knows about this problem.
>>> >>
>>> >>Thanks,
>>> >>
>>> >> - Jan Galkowski.
>>>  [snip]
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   [hidden email]
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.