thr3ads.net - R devel - [Rd] more Matrix weirdness [Sep 2020]

If this information is useful, please help other people find it:
Share via:

Georgi Boshnakov

2020-Sep-09 10:48 UTC

[Rd] more Matrix weirdness

I think that this is because `[<-` dispatches on S4 methods only if the first
argument is S4.
?"[<-" says:

"These operators are also implicit S4 generics, but as primitives,
     S4 methods will be dispatched only on S4 objects ?x?."

Georgi Boshnakov

-----Original Message-----


Message: 19
Date: Tue, 8 Sep 2020 22:04:44 -0400
From: Ben Bolker <bbolker at gmail.com>
To: r-devel <r-devel at r-project.org>
Subject: [Rd] more Matrix weirdness
Message-ID: <fbaf45b7-b6d8-e93f-39d9-aa51d6f2c28e at gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

   Am I being too optimistic in expecting this (mixing and matching 
matrices and Matrices) to work?  If x is a matrix and m is a Matrix, 
replacing a commensurately sized sub-matrix of x with m throws "number 
of items to replace is not a multiple of replacement length" ...

x <- matrix(0,nrow=3,ncol=10, dimnames=list(letters[1:3],LETTERS[1:10]))
rr <- c("a","b","c")
cc <- c("B","C","E")
m <- Matrix(matrix(1:9,3,3))
x[rr,cc] <- m

    cheers
     Ben Bolker




------------------------------

Message: 20
Date: Wed, 9 Sep 2020 07:03:47 +0100
From: Rui Barradas <ruipbarradas at sapo.pt>
To: Ben Bolker <bbolker at gmail.com>, r-devel <r-devel at
r-project.org>
Subject: Re: [Rd] more Matrix weirdness
Message-ID: <7037975c-22b6-6eca-d871-743eead534f2 at sapo.pt>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hello,

R 4.0.2 on Ubuntu 20.04, sessionInfo() below.

I can reproduce this, sort of. The error I'm getting is different:


x[rr, cc] <- m
#Error in x[rr, cc] <- m : replacement has length zero

But if I check lengths and dimensions, they are identical().

identical(length(x[rr, cc]), length(m))
#[1] TRUE
identical(dim(x[rr, cc]), dim(m))
#[1] TRUE


What works is


x[rr, cc] <- as.matrix(m)

I ran Ben's code on RStudio 1.3.1073, the following is run with Rscript 
and the error message is the same.


rui at rui:~$ Rscript --vanilla rhelp.R
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
  [1] LC_CTYPE=pt_PT.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=pt_PT.UTF-8        LC_COLLATE=pt_PT.UTF-8
  [5] LC_MONETARY=pt_PT.UTF-8    LC_MESSAGES=pt_PT.UTF-8
  [7] LC_PAPER=pt_PT.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Matrix_1.2-18

loaded via a namespace (and not attached):
[1] compiler_4.0.2  grid_4.0.2      lattice_0.20-41
Error in x[rr, cc] <- m :
   number of items to replace is not a multiple of replacement length
Execution halted


Hope this helps,

Rui Barradas


?s 03:04 de 09/09/20, Ben Bolker escreveu:>  ? Am I being too optimistic in expecting this (mixing and matching 
> matrices and Matrices) to work?? If x is a matrix and m is a Matrix, 
> replacing a commensurately sized sub-matrix of x with m throws "number
> of items to replace is not a multiple of replacement length" ...
> 
> x <- matrix(0,nrow=3,ncol=10, dimnames=list(letters[1:3],LETTERS[1:10]))
> rr <- c("a","b","c")
> cc <- c("B","C","E")
> m <- Matrix(matrix(1:9,3,3))
> x[rr,cc] <- m
> 
>  ?? cheers
>  ??? Ben Bolker
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



------------------------------

Message: 21
Date: Wed, 9 Sep 2020 08:27:06 +0200
From: Uwe Ligges <ligges at statistik.tu-dortmund.de>
To: r-devel at r-project.org
Subject: Re: [Rd] failing automatic incoming check
Message-ID:
	<fba137f3-e4c4-316e-47ae-ee11b08bc0c2 at statistik.tu-dortmund.de>
Content-Type: text/plain; charset="utf-8"; Format="flowed"



On 08.09.2020 21:34, Sebastian P. Luque wrote:> Hello,
> 
> I got a notification regarding a failure to pass incoming checks
> automatically after a CRAN submission.  The details are given here:
> 
>
https://win-builder.r-project.org/incoming_pretest/diveMove_1.5.0_20200908_191325/
> 
> The only visible issue is a NOTE from the macosx build, with the very
> terse:
> 
> "No Protocol Specified"
> 
> My searches suggest this can be ignored, but it would be nice to squash
> it.  Any tips welcome.
> 

For some reason this should hgave undergone manual inpection but got 
auto rejected. Ideally you would reduce the test timing so that the 
overall check time is less than 10 min .

Best,
Uwe Ligges




------------------------------

Message: 22
Date: Wed, 9 Sep 2020 16:48:40 +1000
From: Hugh Parsonage <hugh.parsonage at gmail.com>
To: Jeroen Ooms <jeroenooms at gmail.com>
Cc: Tomas Kalibera <tomas.kalibera at gmail.com>, Luke Tierney
	<luke-tierney at uiowa.edu>,  R-devel <r-devel at r-project.org>,
Martin
	Maechler <maechler at stat.math.ethz.ch>
Subject: Re: [Rd] [External] Re: Operations with long altrep vectors
	cause segfaults on Windows
Message-ID:
	<CAJmOi+PZcdsLRiBca2_r3dj0RmAJcuFT9FCjkMBjJEdFQ98YTQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I am unable to set break or use gdb with any success when I use that version.

On linux I would do R -d gdb but this gives "unknown option '-d'
"
while gdb R.exe (in the same directory as the debug version) gives the
same output as before.

I'm happy to help but I appreciate this list might not be the best
place to get a tutorial on using gdb on Windows.

On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com>
wrote:>
> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com>
wrote:
> >
> > On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
> > >
> > > On 9/8/20 4:48 PM, Hugh Parsonage wrote:
> > > > Unfortunately I only get
> > > >
> > > > [Thread 21752.0x4aa8 exited with code 3221225477]
> > > > [Thread 21752.0x4514 exited with code 3221225477]
> > > > [Thread 21752.0x3f10 exited with code 3221225477]
> > > > [Inferior 1 (process 21752) exited with code 030000000005]
> > > >
> > > > (I'm guessing I would need to build an instrumented
version of R, or
> > > > can R be debugged using gdb with an off-the-shelf
installation?)
> > >
> > > No, the default build lacks debug symbols. You need a build with
debug
> > > symbols, and if you can reproduce in a build without compiler
> > > optimizations (-O0), the backtrace may be easier to interpret.
Some bugs
> > > however "disappear" when optimizations are disabled.
You can build R
> > > from source (and there may be debug builds provided by someone
else
> > > (Jeroen?)).
> >
> > Debug builds for each revision are available from
> > https://r-devel.github.io . To download the installer you need to
> > click the github icon in the last column in the table. You need to be
> > signed in with a (free) Github account in order to download builds
> > (artifacts) from Github actions. It will show download links for both
> > the regular installer and installer with debug symbols.
> >
> > In other news, the https://r-devel.github.io table also shows that the
> > fix that martin committed is segfaulting on 32-bit.
>
> Sorry that was inaccurate, it is not segfaulting at all, but the unit
> test is raising an error on 32-bit.



------------------------------

Message: 23
Date: Wed, 9 Sep 2020 09:03:05 +0200
From: Tomas Kalibera <tomas.kalibera at gmail.com>
To: Hugh Parsonage <hugh.parsonage at gmail.com>, Jeroen Ooms
	<jeroenooms at gmail.com>
Cc: Luke Tierney <luke-tierney at uiowa.edu>, R-devel
	<r-devel at r-project.org>, Martin Maechler <maechler at
stat.math.ethz.ch>
Subject: Re: [Rd] [External] Re: Operations with long altrep vectors
	cause segfaults on Windows
Message-ID: <3f8e27b4-c6ed-04fe-7878-66d07ddc673f at gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

On 9/9/20 8:48 AM, Hugh Parsonage wrote:> I am unable to set break or use gdb with any success when I use that
version.
>
> On linux I would do R -d gdb but this gives "unknown option
'-d' "
> while gdb R.exe (in the same directory as the debug version) gives the
> same output as before.
>
> I'm happy to help but I appreciate this list might not be the best
> place to get a tutorial on using gdb on Windows.
Essentially, the steps are: build with DEBUG=T (to have debug symbols), 
possibly updating EOPTS in MkRules.local to disable optimizations, then 
run gdb loading RGui, "set solib-search-path", run RGui from gdb. Then
you can break to debugger from RGui menu, or just run the code that 
segfaults, and you get to gdb and can print the stacktrace, etc. You can 
find some information in rw-FAQ (R for Windows FAQ), but yes, it is 
harder than on Linux. We can take care of this report, but of course in 
the longer term it would help if more people could take their time to 
setup debugging and analyze bugs even on Windows.

Tomas
>
> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com>
wrote:
>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at
gmail.com> wrote:
>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
>>>>> Unfortunately I only get
>>>>>
>>>>> [Thread 21752.0x4aa8 exited with code 3221225477]
>>>>> [Thread 21752.0x4514 exited with code 3221225477]
>>>>> [Thread 21752.0x3f10 exited with code 3221225477]
>>>>> [Inferior 1 (process 21752) exited with code 030000000005]
>>>>>
>>>>> (I'm guessing I would need to build an instrumented
version of R, or
>>>>> can R be debugged using gdb with an off-the-shelf
installation?)
>>>> No, the default build lacks debug symbols. You need a build
with debug
>>>> symbols, and if you can reproduce in a build without compiler
>>>> optimizations (-O0), the backtrace may be easier to interpret.
Some bugs
>>>> however "disappear" when optimizations are disabled.
You can build R
>>>> from source (and there may be debug builds provided by someone
else
>>>> (Jeroen?)).
>>> Debug builds for each revision are available from
>>> https://r-devel.github.io . To download the installer you need to
>>> click the github icon in the last column in the table. You need to
be
>>> signed in with a (free) Github account in order to download builds
>>> (artifacts) from Github actions. It will show download links for
both
>>> the regular installer and installer with debug symbols.
>>>
>>> In other news, the https://r-devel.github.io table also shows that
the
>>> fix that martin committed is segfaulting on 32-bit.
>> Sorry that was inaccurate, it is not segfaulting at all, but the unit
>> test is raising an error on 32-bit.



------------------------------

Message: 24
Date: Wed, 9 Sep 2020 17:30:17 +1000
From: Hugh Parsonage <hugh.parsonage at gmail.com>
To: Tomas Kalibera <tomas.kalibera at gmail.com>
Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney
	<luke-tierney at uiowa.edu>,  R-devel <r-devel at r-project.org>,
Martin
	Maechler <maechler at stat.math.ethz.ch>
Subject: Re: [Rd] [External] Re: Operations with long altrep vectors
	cause segfaults on Windows
Message-ID:
	<CAJmOi+MKW_RbxvVOfPDA58aYPzNz8ViKsVa+30ERsjmsV5Je+A at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Thank you!

I get

Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
[New Thread 19940.0x638c]
[New Thread 19940.0x102c]
[New Thread 19940.0x329c]
[New Thread 19940.0x37dc]
warning: Invalid parameter passed to C runtime function.

Program received signal SIGSEGV, Segmentation fault.
0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350,
writeable=<optimized out>) at altclasses.c:169
169     altclasses.c: No such file or directory.

On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at gmail.com>
wrote:>
> On 9/9/20 8:48 AM, Hugh Parsonage wrote:
> > I am unable to set break or use gdb with any success when I use that
version.
> >
> > On linux I would do R -d gdb but this gives "unknown option
'-d' "
> > while gdb R.exe (in the same directory as the debug version) gives the
> > same output as before.
> >
> > I'm happy to help but I appreciate this list might not be the best
> > place to get a tutorial on using gdb on Windows.
>
> Essentially, the steps are: build with DEBUG=T (to have debug symbols),
> possibly updating EOPTS in MkRules.local to disable optimizations, then
> run gdb loading RGui, "set solib-search-path", run RGui from gdb.
Then
> you can break to debugger from RGui menu, or just run the code that
> segfaults, and you get to gdb and can print the stacktrace, etc. You can
> find some information in rw-FAQ (R for Windows FAQ), but yes, it is
> harder than on Linux. We can take care of this report, but of course in
> the longer term it would help if more people could take their time to
> setup debugging and analyze bugs even on Windows.
>
> Tomas
>
> >
> > On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at
gmail.com> wrote:
> >> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at
gmail.com> wrote:
> >>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
> >>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
> >>>>> Unfortunately I only get
> >>>>>
> >>>>> [Thread 21752.0x4aa8 exited with code 3221225477]
> >>>>> [Thread 21752.0x4514 exited with code 3221225477]
> >>>>> [Thread 21752.0x3f10 exited with code 3221225477]
> >>>>> [Inferior 1 (process 21752) exited with code
030000000005]
> >>>>>
> >>>>> (I'm guessing I would need to build an
instrumented version of R, or
> >>>>> can R be debugged using gdb with an off-the-shelf
installation?)
> >>>> No, the default build lacks debug symbols. You need a
build with debug
> >>>> symbols, and if you can reproduce in a build without
compiler
> >>>> optimizations (-O0), the backtrace may be easier to
interpret. Some bugs
> >>>> however "disappear" when optimizations are
disabled. You can build R
> >>>> from source (and there may be debug builds provided by
someone else
> >>>> (Jeroen?)).
> >>> Debug builds for each revision are available from
> >>> https://r-devel.github.io . To download the installer you need
to
> >>> click the github icon in the last column in the table. You
need to be
> >>> signed in with a (free) Github account in order to download
builds
> >>> (artifacts) from Github actions. It will show download links
for both
> >>> the regular installer and installer with debug symbols.
> >>>
> >>> In other news, the https://r-devel.github.io table also shows
that the
> >>> fix that martin committed is segfaulting on 32-bit.
> >> Sorry that was inaccurate, it is not segfaulting at all, but the
unit
> >> test is raising an error on 32-bit.
>
>



------------------------------

Message: 25
Date: Wed, 9 Sep 2020 08:00:41 +0000
From: "Koenker, Roger W" <rkoenker at illinois.edu>
To: r-devel <r-devel at r-project.org>
Subject: [Rd] Environmental Messaging
Message-ID: <6C9F497D-5CEA-4A02-B7AB-490AB4022BB6 at illinois.edu>
Content-Type: text/plain; charset="utf-8"

What sort of message is this to send to the younger generation?
> plastic = 1:5
> card = 1:4
> board = 1:4
> plastic/crossprod(card,board)[1] 0.03333333 0.06666667 0.10000000 0.13333333 0.16666667
Warning message:
In plastic/crossprod(card, board) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

ok,  I can write c(crossprod()) but it is ugly, and environmentally wasteful.
What?s next?  Warnings for my beloved  outer(card, board) * board

------------------------------

Message: 26
Date: Wed, 9 Sep 2020 10:00:55 +0200
From: Tomas Kalibera <tomas.kalibera at gmail.com>
To: Hugh Parsonage <hugh.parsonage at gmail.com>
Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney
	<luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>,
Martin
	Maechler <maechler at stat.math.ethz.ch>
Subject: Re: [Rd] [External] Re: Operations with long altrep vectors
	cause segfaults on Windows
Message-ID: <8383dabf-9093-41ea-2407-8bd75a1009e2 at gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

On 9/9/20 9:30 AM, Hugh Parsonage wrote:> Thank you!
>
> I get
>
> Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
> [New Thread 19940.0x638c]
> [New Thread 19940.0x102c]
> [New Thread 19940.0x329c]
> [New Thread 19940.0x37dc]
> warning: Invalid parameter passed to C runtime function.
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350,
> writeable=<optimized out>) at altclasses.c:169
> 169     altclasses.c: No such file or directory.
Thanks, would you know which svn version this is?

Tomas
>
> On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
>> On 9/9/20 8:48 AM, Hugh Parsonage wrote:
>>> I am unable to set break or use gdb with any success when I use
that version.
>>>
>>> On linux I would do R -d gdb but this gives "unknown option
'-d' "
>>> while gdb R.exe (in the same directory as the debug version) gives
the
>>> same output as before.
>>>
>>> I'm happy to help but I appreciate this list might not be the
best
>>> place to get a tutorial on using gdb on Windows.
>> Essentially, the steps are: build with DEBUG=T (to have debug symbols),
>> possibly updating EOPTS in MkRules.local to disable optimizations, then
>> run gdb loading RGui, "set solib-search-path", run RGui from
gdb. Then
>> you can break to debugger from RGui menu, or just run the code that
>> segfaults, and you get to gdb and can print the stacktrace, etc. You
can
>> find some information in rw-FAQ (R for Windows FAQ), but yes, it is
>> harder than on Linux. We can take care of this report, but of course in
>> the longer term it would help if more people could take their time to
>> setup debugging and analyze bugs even on Windows.
>>
>> Tomas
>>
>>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at
gmail.com> wrote:
>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at
gmail.com> wrote:
>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
>>>>>>> Unfortunately I only get
>>>>>>>
>>>>>>> [Thread 21752.0x4aa8 exited with code 3221225477]
>>>>>>> [Thread 21752.0x4514 exited with code 3221225477]
>>>>>>> [Thread 21752.0x3f10 exited with code 3221225477]
>>>>>>> [Inferior 1 (process 21752) exited with code
030000000005]
>>>>>>>
>>>>>>> (I'm guessing I would need to build an
instrumented version of R, or
>>>>>>> can R be debugged using gdb with an off-the-shelf
installation?)
>>>>>> No, the default build lacks debug symbols. You need a
build with debug
>>>>>> symbols, and if you can reproduce in a build without
compiler
>>>>>> optimizations (-O0), the backtrace may be easier to
interpret. Some bugs
>>>>>> however "disappear" when optimizations are
disabled. You can build R
>>>>>> from source (and there may be debug builds provided by
someone else
>>>>>> (Jeroen?)).
>>>>> Debug builds for each revision are available from
>>>>> https://r-devel.github.io . To download the installer you
need to
>>>>> click the github icon in the last column in the table. You
need to be
>>>>> signed in with a (free) Github account in order to download
builds
>>>>> (artifacts) from Github actions. It will show download
links for both
>>>>> the regular installer and installer with debug symbols.
>>>>>
>>>>> In other news, the https://r-devel.github.io table also
shows that the
>>>>> fix that martin committed is segfaulting on 32-bit.
>>>> Sorry that was inaccurate, it is not segfaulting at all, but
the unit
>>>> test is raising an error on 32-bit.
>>



------------------------------

Message: 27
Date: Wed, 9 Sep 2020 18:32:58 +1000
From: Hugh Parsonage <hugh.parsonage at gmail.com>
To: Tomas Kalibera <tomas.kalibera at gmail.com>
Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney
	<luke-tierney at uiowa.edu>,  R-devel <r-devel at r-project.org>,
Martin
	Maechler <maechler at stat.math.ethz.ch>
Subject: Re: [Rd] [External] Re: Operations with long altrep vectors
	cause segfaults on Windows
Message-ID:
	<CAJmOi+MLyn_WcBLFSQdL9ze4iDzazysPcU7QGOQtWryTod44Yg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

R Under development (unstable) (2020-09-08 r79165)

On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera <tomas.kalibera at gmail.com>
wrote:>
> On 9/9/20 9:30 AM, Hugh Parsonage wrote:
> > Thank you!
> >
> > I get
> >
> > Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
> > [New Thread 19940.0x638c]
> > [New Thread 19940.0x102c]
> > [New Thread 19940.0x329c]
> > [New Thread 19940.0x37dc]
> > warning: Invalid parameter passed to C runtime function.
> >
> > Program received signal SIGSEGV, Segmentation fault.
> > 0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350,
> > writeable=<optimized out>) at altclasses.c:169
> > 169     altclasses.c: No such file or directory.
>
> Thanks, would you know which svn version this is?
>
> Tomas
>
> >
> > On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
> >> On 9/9/20 8:48 AM, Hugh Parsonage wrote:
> >>> I am unable to set break or use gdb with any success when I
use that version.
> >>>
> >>> On linux I would do R -d gdb but this gives "unknown
option '-d' "
> >>> while gdb R.exe (in the same directory as the debug version)
gives the
> >>> same output as before.
> >>>
> >>> I'm happy to help but I appreciate this list might not be
the best
> >>> place to get a tutorial on using gdb on Windows.
> >> Essentially, the steps are: build with DEBUG=T (to have debug
symbols),
> >> possibly updating EOPTS in MkRules.local to disable optimizations,
then
> >> run gdb loading RGui, "set solib-search-path", run RGui
from gdb. Then
> >> you can break to debugger from RGui menu, or just run the code
that
> >> segfaults, and you get to gdb and can print the stacktrace, etc.
You can
> >> find some information in rw-FAQ (R for Windows FAQ), but yes, it
is
> >> harder than on Linux. We can take care of this report, but of
course in
> >> the longer term it would help if more people could take their time
to
> >> setup debugging and analyze bugs even on Windows.
> >>
> >> Tomas
> >>
> >>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at
gmail.com> wrote:
> >>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms
at gmail.com> wrote:
> >>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
> >>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
> >>>>>>> Unfortunately I only get
> >>>>>>>
> >>>>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
> >>>>>>> [Thread 21752.0x4514 exited with code
3221225477]
> >>>>>>> [Thread 21752.0x3f10 exited with code
3221225477]
> >>>>>>> [Inferior 1 (process 21752) exited with code
030000000005]
> >>>>>>>
> >>>>>>> (I'm guessing I would need to build an
instrumented version of R, or
> >>>>>>> can R be debugged using gdb with an
off-the-shelf installation?)
> >>>>>> No, the default build lacks debug symbols. You
need a build with debug
> >>>>>> symbols, and if you can reproduce in a build
without compiler
> >>>>>> optimizations (-O0), the backtrace may be easier
to interpret. Some bugs
> >>>>>> however "disappear" when optimizations
are disabled. You can build R
> >>>>>> from source (and there may be debug builds
provided by someone else
> >>>>>> (Jeroen?)).
> >>>>> Debug builds for each revision are available from
> >>>>> https://r-devel.github.io . To download the installer
you need to
> >>>>> click the github icon in the last column in the table.
You need to be
> >>>>> signed in with a (free) Github account in order to
download builds
> >>>>> (artifacts) from Github actions. It will show download
links for both
> >>>>> the regular installer and installer with debug
symbols.
> >>>>>
> >>>>> In other news, the https://r-devel.github.io table
also shows that the
> >>>>> fix that martin committed is segfaulting on 32-bit.
> >>>> Sorry that was inaccurate, it is not segfaulting at all,
but the unit
> >>>> test is raising an error on 32-bit.
> >>
>



------------------------------

Message: 28
Date: Wed, 9 Sep 2020 10:53:18 +0200
From: Tomas Kalibera <tomas.kalibera at gmail.com>
To: Hugh Parsonage <hugh.parsonage at gmail.com>
Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney
	<luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>,
Martin
	Maechler <maechler at stat.math.ethz.ch>
Subject: Re: [Rd] [External] Re: Operations with long altrep vectors
	cause segfaults on Windows
Message-ID: <6b01fb27-ec83-4dea-6478-c344f285083b at gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Thanks. Should be now fixed in 79169.
Tomas

On 9/9/20 10:32 AM, Hugh Parsonage wrote:> R Under development (unstable) (2020-09-08 r79165)
>
> On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
>> On 9/9/20 9:30 AM, Hugh Parsonage wrote:
>>> Thank you!
>>>
>>> I get
>>>
>>> Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
>>> [New Thread 19940.0x638c]
>>> [New Thread 19940.0x102c]
>>> [New Thread 19940.0x329c]
>>> [New Thread 19940.0x37dc]
>>> warning: Invalid parameter passed to C runtime function.
>>>
>>> Program received signal SIGSEGV, Segmentation fault.
>>> 0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350,
>>> writeable=<optimized out>) at altclasses.c:169
>>> 169     altclasses.c: No such file or directory.
>> Thanks, would you know which svn version this is?
>>
>> Tomas
>>
>>> On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
>>>> On 9/9/20 8:48 AM, Hugh Parsonage wrote:
>>>>> I am unable to set break or use gdb with any success when I
use that version.
>>>>>
>>>>> On linux I would do R -d gdb but this gives "unknown
option '-d' "
>>>>> while gdb R.exe (in the same directory as the debug
version) gives the
>>>>> same output as before.
>>>>>
>>>>> I'm happy to help but I appreciate this list might not
be the best
>>>>> place to get a tutorial on using gdb on Windows.
>>>> Essentially, the steps are: build with DEBUG=T (to have debug
symbols),
>>>> possibly updating EOPTS in MkRules.local to disable
optimizations, then
>>>> run gdb loading RGui, "set solib-search-path", run
RGui from gdb. Then
>>>> you can break to debugger from RGui menu, or just run the code
that
>>>> segfaults, and you get to gdb and can print the stacktrace,
etc. You can
>>>> find some information in rw-FAQ (R for Windows FAQ), but yes,
it is
>>>> harder than on Linux. We can take care of this report, but of
course in
>>>> the longer term it would help if more people could take their
time to
>>>> setup debugging and analyze bugs even on Windows.
>>>>
>>>> Tomas
>>>>
>>>>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at
gmail.com> wrote:
>>>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
<jeroenooms at gmail.com> wrote:
>>>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
>>>>>>>>> Unfortunately I only get
>>>>>>>>>
>>>>>>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
>>>>>>>>> [Thread 21752.0x4514 exited with code
3221225477]
>>>>>>>>> [Thread 21752.0x3f10 exited with code
3221225477]
>>>>>>>>> [Inferior 1 (process 21752) exited with
code 030000000005]
>>>>>>>>>
>>>>>>>>> (I'm guessing I would need to build an
instrumented version of R, or
>>>>>>>>> can R be debugged using gdb with an
off-the-shelf installation?)
>>>>>>>> No, the default build lacks debug symbols. You
need a build with debug
>>>>>>>> symbols, and if you can reproduce in a build
without compiler
>>>>>>>> optimizations (-O0), the backtrace may be
easier to interpret. Some bugs
>>>>>>>> however "disappear" when
optimizations are disabled. You can build R
>>>>>>>> from source (and there may be debug builds
provided by someone else
>>>>>>>> (Jeroen?)).
>>>>>>> Debug builds for each revision are available from
>>>>>>> https://r-devel.github.io . To download the
installer you need to
>>>>>>> click the github icon in the last column in the
table. You need to be
>>>>>>> signed in with a (free) Github account in order to
download builds
>>>>>>> (artifacts) from Github actions. It will show
download links for both
>>>>>>> the regular installer and installer with debug
symbols.
>>>>>>>
>>>>>>> In other news, the https://r-devel.github.io table
also shows that the
>>>>>>> fix that martin committed is segfaulting on 32-bit.
>>>>>> Sorry that was inaccurate, it is not segfaulting at
all, but the unit
>>>>>> test is raising an error on 32-bit.



------------------------------

Message: 29
Date: Wed, 9 Sep 2020 11:06:12 +0200
From: Tomas Kalibera <tomas.kalibera at gmail.com>
To: Jeroen Ooms <jeroenooms at gmail.com>
Cc: Hugh Parsonage <hugh.parsonage at gmail.com>, Luke Tierney
	<luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>,
Martin
	Maechler <maechler at stat.math.ethz.ch>
Subject: Re: [Rd] [External] Re: Operations with long altrep vectors
	cause segfaults on Windows
Message-ID: <5fd517e2-ad46-c343-2a63-cda01ff58acc at gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

On 9/8/20 11:47 PM, Jeroen Ooms wrote:> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com>
wrote:
>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
>>>> Unfortunately I only get
>>>>
>>>> [Thread 21752.0x4aa8 exited with code 3221225477]
>>>> [Thread 21752.0x4514 exited with code 3221225477]
>>>> [Thread 21752.0x3f10 exited with code 3221225477]
>>>> [Inferior 1 (process 21752) exited with code 030000000005]
>>>>
>>>> (I'm guessing I would need to build an instrumented version
of R, or
>>>> can R be debugged using gdb with an off-the-shelf
installation?)
>>> No, the default build lacks debug symbols. You need a build with
debug
>>> symbols, and if you can reproduce in a build without compiler
>>> optimizations (-O0), the backtrace may be easier to interpret. Some
bugs
>>> however "disappear" when optimizations are disabled. You
can build R
>>> from source (and there may be debug builds provided by someone else
>>> (Jeroen?)).
>> Debug builds for each revision are available from
>> https://r-devel.github.io . To download the installer you need to
>> click the github icon in the last column in the table. You need to be
>> signed in with a (free) Github account in order to download builds
>> (artifacts) from Github actions. It will show download links for both
>> the regular installer and installer with debug symbols.
>>
>> In other news, the https://r-devel.github.io table also shows that the
>> fix that martin committed is segfaulting on 32-bit.
> Sorry that was inaccurate, it is not segfaulting at all, but the unit
> test is raising an error on 32-bit.
Now fixed, the test needs to be run only on 64-bit builds where such 
long vectors/sequences are allowed.

Tomas




------------------------------

Subject: Digest Footer

_______________________________________________
R-devel at r-project.org mailing list  DIGESTED
https://stat.ethz.ch/mailman/listinfo/r-devel


------------------------------

End of R-devel Digest, Vol 211, Issue 7
***************************************

Martin Maechler

2020-Sep-10 12:48 UTC

head link

[Rd] more Matrix weirdness

>>>>> Georgi Boshnakov 
>>>>>     on Wed, 9 Sep 2020 10:48:56 +0000 writes:
    > I think that this is because `[<-` dispatches on S4
    > methods only if the first argument is S4.  ?"[<-" says:

    > "These operators are also implicit S4 generics, but as
    > primitives, S4 methods will be dispatched only on S4
    > objects ?x?."

    > Georgi Boshnakov

Yes, exactly,  very well found, Georgi!

This is something I would have wanted different for years,
exactly because of several such problems with the Matrix
package of which I'm the maintainer.

Long time ago I had also looked if I saw how to fix this
behavior inside 'methods' (i.e. the S4 infrastructure pkg)
and I think in this case also, inside R's basic C code.

At the time (~ 10 yrs ago) I gave up, but don't remember why.

I'm happy if you create a formal bug report, possibly "wishlist"
as it is documented behavior, for this infelicity...
and then I will probably add the  'HELPWANTED'  keyword.

Martin


    > -----Original Message-----


    > Message: 19 Date: Tue, 8 Sep 2020 22:04:44 -0400 From: Ben
    > Bolker <bbolker at gmail.com> To: r-devel
    > <r-devel at r-project.org> Subject: [Rd] more Matrix
    > weirdness Message-ID:
    > <fbaf45b7-b6d8-e93f-39d9-aa51d6f2c28e at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    >    Am I being too optimistic in expecting this (mixing and
    > matching matrices and Matrices) to work?  If x is a matrix
    > and m is a Matrix, replacing a commensurately sized
    > sub-matrix of x with m throws "number of items to replace
    > is not a multiple of replacement length" ...

    > x <- matrix(0,nrow=3,ncol=10,
    > dimnames=list(letters[1:3],LETTERS[1:10])) rr <-
    > c("a","b","c") cc <-
c("B","C","E") m <-
    > Matrix(matrix(1:9,3,3)) x[rr,cc] <- m

    >     cheers Ben Bolker




    > ------------------------------

    > Message: 20 Date: Wed, 9 Sep 2020 07:03:47 +0100 From: Rui
    > Barradas <ruipbarradas at sapo.pt> To: Ben Bolker
    > <bbolker at gmail.com>, r-devel <r-devel at r-project.org>
    > Subject: Re: [Rd] more Matrix weirdness Message-ID:
    > <7037975c-22b6-6eca-d871-743eead534f2 at sapo.pt>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > Hello,

    > R 4.0.2 on Ubuntu 20.04, sessionInfo() below.

    > I can reproduce this, sort of. The error I'm getting is
    > different:


    > x[rr, cc] <- m #Error in x[rr, cc] <- m : replacement has
    > length zero

    > But if I check lengths and dimensions, they are
    > identical().

    > identical(length(x[rr, cc]), length(m)) #[1] TRUE
    > identical(dim(x[rr, cc]), dim(m)) #[1] TRUE


    > What works is


    > x[rr, cc] <- as.matrix(m)

    > I ran Ben's code on RStudio 1.3.1073, the following is run
    > with Rscript and the error message is the same.


    > rui at rui:~$ Rscript --vanilla rhelp.R R version 4.0.2
    > (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit)
    > Running under: Ubuntu 20.04.1 LTS

    > Matrix products: default BLAS:
    > /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK:
    > /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

    > locale: [1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C [3]
    > LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8 [5]
    > LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8 [7]
    > LC_PAPER=pt_PT.UTF-8 LC_NAME=C [9] LC_ADDRESS=C
    > LC_TELEPHONE=C [11] LC_MEASUREMENT=pt_PT.UTF-8
    > LC_IDENTIFICATION=C

    > attached base packages: [1] stats graphics grDevices utils
    > datasets methods base

    > other attached packages: [1] Matrix_1.2-18

    > loaded via a namespace (and not attached): [1]
    > compiler_4.0.2 grid_4.0.2 lattice_0.20-41 Error in x[rr,
    > cc] <- m : number of items to replace is not a multiple of
    > replacement length Execution halted


    > Hope this helps,

    > Rui Barradas


    > ?s 03:04 de 09/09/20, Ben Bolker escreveu:
    >> ? Am I being too optimistic in expecting this (mixing and
    >> matching matrices and Matrices) to work?? If x is a
    >> matrix and m is a Matrix, replacing a commensurately
    >> sized sub-matrix of x with m throws "number of items to
    >> replace is not a multiple of replacement length" ...
    >> 
    >> x <- matrix(0,nrow=3,ncol=10,
    >> dimnames=list(letters[1:3],LETTERS[1:10])) rr <-
    >> c("a","b","c") cc <-
c("B","C","E") m <-
    >> Matrix(matrix(1:9,3,3)) x[rr,cc] <- m
    >> 
    >> ?? cheers ??? Ben Bolker
    >> 
    >> ______________________________________________
    >> R-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel




    > ------------------------------

    > Message: 21 Date: Wed, 9 Sep 2020 08:27:06 +0200 From: Uwe
    > Ligges <ligges at statistik.tu-dortmund.de> To:
    > r-devel at r-project.org Subject: Re: [Rd] failing automatic
    > incoming check Message-ID:
    > <fba137f3-e4c4-316e-47ae-ee11b08bc0c2 at
statistik.tu-dortmund.de>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"



    > On 08.09.2020 21:34, Sebastian P. Luque wrote:
    >> Hello,
    >> 
    >> I got a notification regarding a failure to pass incoming
    >> checks automatically after a CRAN submission.  The
    >> details are given here:
    >> 
    >>
https://win-builder.r-project.org/incoming_pretest/diveMove_1.5.0_20200908_191325/
    >> 
    >> The only visible issue is a NOTE from the macosx build,
    >> with the very terse:
    >> 
    >> "No Protocol Specified"
    >> 
    >> My searches suggest this can be ignored, but it would be
    >> nice to squash it.  Any tips welcome.
    >> 


    > For some reason this should hgave undergone manual
    > inpection but got auto rejected. Ideally you would reduce
    > the test timing so that the overall check time is less
    > than 10 min .

    > Best, Uwe Ligges




    > ------------------------------

    > Message: 22 Date: Wed, 9 Sep 2020 16:48:40 +1000 From:
    > Hugh Parsonage <hugh.parsonage at gmail.com> To: Jeroen Ooms
    > <jeroenooms at gmail.com> Cc: Tomas Kalibera
    > <tomas.kalibera at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <CAJmOi+PZcdsLRiBca2_r3dj0RmAJcuFT9FCjkMBjJEdFQ98YTQ at
mail.gmail.com>
    > Content-Type: text/plain; charset="utf-8"

    > I am unable to set break or use gdb with any success when
    > I use that version.

    > On linux I would do R -d gdb but this gives "unknown
    > option '-d' " while gdb R.exe (in the same directory as
    > the debug version) gives the same output as before.

    > I'm happy to help but I appreciate this list might not be
    > the best place to get a tutorial on using gdb on Windows.

    > On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    > <jeroenooms at gmail.com> wrote:
    >> 
    >> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote:
    >> >
    >> > On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote:
    >> > >
    >> > > On 9/8/20 4:48 PM, Hugh Parsonage wrote: > > >
    >> Unfortunately I only get
    >> > > >
    >> > > > [Thread 21752.0x4aa8 exited with code 3221225477]
>
    >> > > [Thread 21752.0x4514 exited with code 3221225477] >
>
    >> > [Thread 21752.0x3f10 exited with code 3221225477] > >
>
    >> [Inferior 1 (process 21752) exited with code
    >> 030000000005]
    >> > > >
    >> > > > (I'm guessing I would need to build an
instrumented
    >> version of R, or > > > can R be debugged using gdb with
    >> an off-the-shelf installation?)
    >> > >
    >> > > No, the default build lacks debug symbols. You need a
    >> build with debug > > symbols, and if you can reproduce in
    >> a build without compiler > > optimizations (-O0), the
    >> backtrace may be easier to interpret. Some bugs > >
    >> however "disappear" when optimizations are disabled. You
    >> can build R > > from source (and there may be debug
    >> builds provided by someone else > > (Jeroen?)).
    >> >
    >> > Debug builds for each revision are available from >
    >> https://r-devel.github.io . To download the installer you
    >> need to > click the github icon in the last column in the
    >> table. You need to be > signed in with a (free) Github
    >> account in order to download builds > (artifacts) from
    >> Github actions. It will show download links for both >
    >> the regular installer and installer with debug symbols.
    >> >
    >> > In other news, the https://r-devel.github.io table also
    >> shows that the > fix that martin committed is segfaulting
    >> on 32-bit.
    >> 
    >> Sorry that was inaccurate, it is not segfaulting at all,
    >> but the unit test is raising an error on 32-bit.




    > ------------------------------

    > Message: 23 Date: Wed, 9 Sep 2020 09:03:05 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh
    > Parsonage <hugh.parsonage at gmail.com>, Jeroen Ooms
    > <jeroenooms at gmail.com> Cc: Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <3f8e27b4-c6ed-04fe-7878-66d07ddc673f at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > On 9/9/20 8:48 AM, Hugh Parsonage wrote:
    >> I am unable to set break or use gdb with any success when
    >> I use that version.
    >> 
    >> On linux I would do R -d gdb but this gives "unknown
    >> option '-d' " while gdb R.exe (in the same directory
as
    >> the debug version) gives the same output as before.
    >> 
    >> I'm happy to help but I appreciate this list might not be
    >> the best place to get a tutorial on using gdb on Windows.

    > Essentially, the steps are: build with DEBUG=T (to have
    > debug symbols), possibly updating EOPTS in MkRules.local
    > to disable optimizations, then run gdb loading RGui, "set
    > solib-search-path", run RGui from gdb. Then you can break
    > to debugger from RGui menu, or just run the code that
    > segfaults, and you get to gdb and can print the
    > stacktrace, etc. You can find some information in rw-FAQ
    > (R for Windows FAQ), but yes, it is harder than on
    > Linux. We can take care of this report, but of course in
    > the longer term it would help if more people could take
    > their time to setup debugging and analyze bugs even on
    > Windows.

    > Tomas

    >> 
    >> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote:
    >>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >>> <jeroenooms at gmail.com> wrote:
    >>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >>>> <tomas.kalibera at gmail.com> wrote:
    >>>>> On 9/8/20 4:48 PM, Hugh Parsonage
wrote:>>>>> Unfortunately I only get
    >>>>>> >>>>> [Thread 21752.0x4aa8 exited with code 3221225477]
>>>>> [Thread 21752.0x4514 exited with code 3221225477]
>>>>> [Thread 21752.0x3f10 exited with code 3221225477]
>>>>> [Inferior 1 (process 21752) exited with code 030000000005]
    >>>>>> >>>>> (I'm guessing I would need to build an instrumented
    >>>>>> version of R, or>>>>> can R be debugged using gdb with an off-the-shelf    >>>>>> installation?)
    >>>>> No, the default build lacks debug symbols. You need a
    >>>>> build with debug symbols, and if you can reproduce in
    >>>>> a build without compiler optimizations (-O0), the
    >>>>> backtrace may be easier to interpret. Some bugs
    >>>>> however "disappear" when optimizations are
    >>>>> disabled. You can build R from source (and there may
    >>>>> be debug builds provided by someone else (Jeroen?)).
    >>>> Debug builds for each revision are available from
    >>>> https://r-devel.github.io . To download the installer
    >>>> you need to click the github icon in the last column in
    >>>> the table. You need to be signed in with a (free)
    >>>> Github account in order to download builds (artifacts)
    >>>> from Github actions. It will show download links for
    >>>> both the regular installer and installer with debug
    >>>> symbols.
    >>>> 
    >>>> In other news, the https://r-devel.github.io table also
    >>>> shows that the fix that martin committed is segfaulting
    >>>> on 32-bit.
    >>> Sorry that was inaccurate, it is not segfaulting at all,
    >>> but the unit test is raising an error on 32-bit.




    > ------------------------------

    > Message: 24 Date: Wed, 9 Sep 2020 17:30:17 +1000 From:
    > Hugh Parsonage <hugh.parsonage at gmail.com> To: Tomas
    > Kalibera <tomas.kalibera at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <CAJmOi+MKW_RbxvVOfPDA58aYPzNz8ViKsVa+30ERsjmsV5Je+A at
mail.gmail.com>
    > Content-Type: text/plain; charset="utf-8"

    > Thank you!

    > I get

    > Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
    > [New Thread 19940.0x638c] [New Thread 19940.0x102c] [New
    > Thread 19940.0x329c] [New Thread 19940.0x37dc] warning:
    > Invalid parameter passed to C runtime function.

    > Program received signal SIGSEGV, Segmentation fault.
    > 0x000000006c72d206 in compact_intseq_Dataptr
    > (x=0x12783350, writeable=<optimized out>) at
    > altclasses.c:169 169 altclasses.c: No such file or
    > directory.

    > On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    > <tomas.kalibera at gmail.com> wrote:
    >> 
    >> On 9/9/20 8:48 AM, Hugh Parsonage wrote: > I am unable to
    >> set break or use gdb with any success when I use that
    >> version.
    >> >
    >> > On linux I would do R -d gdb but this gives "unknown
    >> option '-d' " > while gdb R.exe (in the same
directory as
    >> the debug version) gives the > same output as before.
    >> >
    >> > I'm happy to help but I appreciate this list might not
    >> be the best > place to get a tutorial on using gdb on
    >> Windows.
    >> 
    >> Essentially, the steps are: build with DEBUG=T (to have
    >> debug symbols), possibly updating EOPTS in MkRules.local
    >> to disable optimizations, then run gdb loading RGui, "set
    >> solib-search-path", run RGui from gdb. Then you can break
    >> to debugger from RGui menu, or just run the code that
    >> segfaults, and you get to gdb and can print the
    >> stacktrace, etc. You can find some information in rw-FAQ
    >> (R for Windows FAQ), but yes, it is harder than on
    >> Linux. We can take care of this report, but of course in
    >> the longer term it would help if more people could take
    >> their time to setup debugging and analyze bugs even on
    >> Windows.
    >> 
    >> Tomas
    >> 
    >> >
    >> > On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote: >> On Tue, Sep 8, 2020
at
    >> 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote:
>>> On
    >> Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote: >>>> On
9/8/20 4:48 PM,
    >> Hugh Parsonage wrote: >>>>> Unfortunately I only get
    >> >>>>>
    >> >>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
    >> >>>>> [Thread 21752.0x4514 exited with code
3221225477]
    >> >>>>> [Thread 21752.0x3f10 exited with code
3221225477]
    >> >>>>> [Inferior 1 (process 21752) exited with code
    >> 030000000005]
    >> >>>>>
    >> >>>>> (I'm guessing I would need to build an
instrumented
    >> version of R, or >>>>> can R be debugged using gdb
with
    >> an off-the-shelf installation?)  >>>> No, the default
    >> build lacks debug symbols. You need a build with debug
    >> >>>> symbols, and if you can reproduce in a build
without
    >> compiler >>>> optimizations (-O0), the backtrace may be
    >> easier to interpret. Some bugs >>>> however
"disappear"
    >> when optimizations are disabled. You can build R >>>>
    >> from source (and there may be debug builds provided by
    >> someone else >>>> (Jeroen?)).  >>> Debug
builds for each
    >> revision are available from >>> https://r-devel.github.io
    >> . To download the installer you need to >>> click the
    >> github icon in the last column in the table. You need to
    >> be >>> signed in with a (free) Github account in order to
    >> download builds >>> (artifacts) from Github actions. It
    >> will show download links for both >>> the regular
    >> installer and installer with debug symbols.
    >> >>>
    >> >>> In other news, the https://r-devel.github.io table
    >> also shows that the >>> fix that martin committed is
    >> segfaulting on 32-bit.  >> Sorry that was inaccurate, it
    >> is not segfaulting at all, but the unit >> test is
    >> raising an error on 32-bit.
    >> 
    >> 




    > ------------------------------

    > Message: 25 Date: Wed, 9 Sep 2020 08:00:41 +0000 From:
    > "Koenker, Roger W" <rkoenker at illinois.edu> To:
r-devel
    > <r-devel at r-project.org> Subject: [Rd] Environmental
    > Messaging Message-ID:
    > <6C9F497D-5CEA-4A02-B7AB-490AB4022BB6 at illinois.edu>
    > Content-Type: text/plain; charset="utf-8"

    > What sort of message is this to send to the younger
    > generation?

    >> plastic = 1:5 card = 1:4 board = 1:4
    >> plastic/crossprod(card,board)
    > [1] 0.03333333 0.06666667 0.10000000 0.13333333 0.16666667
    > Warning message: In plastic/crossprod(card, board) :
    > Recycling array of length 1 in vector-array arithmetic is
    > deprecated.  Use c() or as.vector() instead.

    > ok, I can write c(crossprod()) but it is ugly, and
    > environmentally wasteful.  What?s next?  Warnings for my
    > beloved outer(card, board) * board

    > ------------------------------

    > Message: 26 Date: Wed, 9 Sep 2020 10:00:55 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh
    > Parsonage <hugh.parsonage at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <8383dabf-9093-41ea-2407-8bd75a1009e2 at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > On 9/9/20 9:30 AM, Hugh Parsonage wrote:
    >> Thank you!
    >> 
    >> I get
    >> 
    >> Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
    >> [New Thread 19940.0x638c] [New Thread 19940.0x102c] [New
    >> Thread 19940.0x329c] [New Thread 19940.0x37dc] warning:
    >> Invalid parameter passed to C runtime function.
    >> 
    >> Program received signal SIGSEGV, Segmentation fault.
    >> 0x000000006c72d206 in compact_intseq_Dataptr
    >> (x=0x12783350, writeable=<optimized out>) at
    >> altclasses.c:169 169 altclasses.c: No such file or
    >> directory.

    > Thanks, would you know which svn version this is?

    > Tomas

    >> 
    >> On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote:
    >>> On 9/9/20 8:48 AM, Hugh Parsonage wrote:
    >>>> I am unable to set break or use gdb with any success
    >>>> when I use that version.
    >>>> 
    >>>> On linux I would do R -d gdb but this gives "unknown
    >>>> option '-d' " while gdb R.exe (in the same
directory as
    >>>> the debug version) gives the same output as before.
    >>>> 
    >>>> I'm happy to help but I appreciate this list might not
    >>>> be the best place to get a tutorial on using gdb on
    >>>> Windows.
    >>> Essentially, the steps are: build with DEBUG=T (to have
    >>> debug symbols), possibly updating EOPTS in MkRules.local
    >>> to disable optimizations, then run gdb loading RGui,
    >>> "set solib-search-path", run RGui from gdb. Then you
can
    >>> break to debugger from RGui menu, or just run the code
    >>> that segfaults, and you get to gdb and can print the
    >>> stacktrace, etc. You can find some information in rw-FAQ
    >>> (R for Windows FAQ), but yes, it is harder than on
    >>> Linux. We can take care of this report, but of course in
    >>> the longer term it would help if more people could take
    >>> their time to setup debugging and analyze bugs even on
    >>> Windows.
    >>> 
    >>> Tomas
    >>> 
    >>>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >>>> <jeroenooms at gmail.com> wrote:
    >>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >>>>> <jeroenooms at gmail.com>
wrote:>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera    >>>>> <tomas.kalibera at gmail.com> wrote:
    >>>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
    >>>>>>>> Unfortunately I only get
    >>>>>>>> 
    >>>>>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
    >>>>>>>> [Thread 21752.0x4514 exited with code
3221225477]
    >>>>>>>> [Thread 21752.0x3f10 exited with code
3221225477]
    >>>>>>>> [Inferior 1 (process 21752) exited with
code
    >>>>>>>> 030000000005]
    >>>>>>>> 
    >>>>>>>> (I'm guessing I would need to build an
instrumented
    >>>>>>>> version of R, or can R be debugged using
gdb with
    >>>>>>>> an off-the-shelf installation?)
    >>>>>>> No, the default build lacks debug symbols. You
need
    >>>>>>> a build with debug symbols, and if you can
reproduce
    >>>>>>> in a build without compiler optimizations
(-O0), the
    >>>>>>> backtrace may be easier to interpret. Some bugs
    >>>>>>> however "disappear" when
optimizations are
    >>>>>>> disabled. You can build R from source (and
there may
    >>>>>>> be debug builds provided by someone else
(Jeroen?)).>>>>> Debug builds for each revision are available from
>>>>> https://r-devel.github.io . To download the installer you
    >>>>>>> need to>>>>> click the github icon in the last column in the table. You
    >>>>>>> need to be>>>>> signed in with a (free) Github account in order to
    >>>>>>> download builds>>>>> (artifacts) from Github actions. It will show download
    >>>>>>> links for both>>>>> the regular installer and installer with debug symbols.
    >>>>>> >>>>> In other news, the https://r-devel.github.io table also
    >>>>>> shows that the>>>>> fix that martin committed is segfaulting on 32-bit.    >>>>> Sorry that was inaccurate, it is not segfaulting at
    >>>>> all, but the unit test is raising an error on 32-bit.
    >>> 




    > ------------------------------

    > Message: 27 Date: Wed, 9 Sep 2020 18:32:58 +1000 From:
    > Hugh Parsonage <hugh.parsonage at gmail.com> To: Tomas
    > Kalibera <tomas.kalibera at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <CAJmOi+MLyn_WcBLFSQdL9ze4iDzazysPcU7QGOQtWryTod44Yg at
mail.gmail.com>
    > Content-Type: text/plain; charset="utf-8"

    > R Under development (unstable) (2020-09-08 r79165)

    > On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera
    > <tomas.kalibera at gmail.com> wrote:
    >> 
    >> On 9/9/20 9:30 AM, Hugh Parsonage wrote: > Thank you!
    >> >
    >> > I get
    >> >
    >> > Starting program:
    >> C:\R\R-devel-20200909\bin\x64\Rgui.exe > [New Thread
    >> 19940.0x638c] > [New Thread 19940.0x102c] > [New Thread
    >> 19940.0x329c] > [New Thread 19940.0x37dc] > warning:
    >> Invalid parameter passed to C runtime function.
    >> >
    >> > Program received signal SIGSEGV, Segmentation fault.  >
    >> 0x000000006c72d206 in compact_intseq_Dataptr
    >> (x=0x12783350, > writeable=<optimized out>) at
    >> altclasses.c:169 > 169 altclasses.c: No such file or
    >> directory.
    >> 
    >> Thanks, would you know which svn version this is?
    >> 
    >> Tomas
    >> 
    >> >
    >> > On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote: >> On 9/9/20 8:48
AM,
    >> Hugh Parsonage wrote: >>> I am unable to set break or use
    >> gdb with any success when I use that version.
    >> >>>
    >> >>> On linux I would do R -d gdb but this gives
"unknown
    >> option '-d' " >>> while gdb R.exe (in the
same directory
    >> as the debug version) gives the >>> same output as
    >> before.
    >> >>>
    >> >>> I'm happy to help but I appreciate this list might
    >> not be the best >>> place to get a tutorial on using gdb
    >> on Windows.  >> Essentially, the steps are: build with
    >> DEBUG=T (to have debug symbols), >> possibly updating
    >> EOPTS in MkRules.local to disable optimizations, then >>
    >> run gdb loading RGui, "set solib-search-path", run RGui
    >> from gdb. Then >> you can break to debugger from RGui
    >> menu, or just run the code that >> segfaults, and you get
    >> to gdb and can print the stacktrace, etc. You can >> find
    >> some information in rw-FAQ (R for Windows FAQ), but yes,
    >> it is >> harder than on Linux. We can take care of this
    >> report, but of course in >> the longer term it would help
    >> if more people could take their time to >> setup
    >> debugging and analyze bugs even on Windows.
    >> >>
    >> >> Tomas
    >> >>
    >> >>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote: >>>> On Tue, Sep
8, 2020 at
    >> 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote:
>>>>>
    >> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote: >>>>>>
On 9/8/20 4:48
    >> PM, Hugh Parsonage wrote: >>>>>>>
Unfortunately I only
    >> get
    >> >>>>>>>
    >> >>>>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
    >> >>>>>>> [Thread 21752.0x4514 exited with code
3221225477]
    >> >>>>>>> [Thread 21752.0x3f10 exited with code
3221225477]
    >> >>>>>>> [Inferior 1 (process 21752) exited
with code
    >> 030000000005]
    >> >>>>>>>
    >> >>>>>>> (I'm guessing I would need to
build an
    >> instrumented version of R, or >>>>>>> can R be
debugged
    >> using gdb with an off-the-shelf installation?) 
>>>>>>
    >> No, the default build lacks debug symbols. You need a
    >> build with debug >>>>>> symbols, and if you can
reproduce
    >> in a build without compiler >>>>>> optimizations
(-O0),
    >> the backtrace may be easier to interpret. Some bugs
    >> >>>>>> however "disappear" when
optimizations are
    >> disabled. You can build R >>>>>> from source (and
there
    >> may be debug builds provided by someone else
>>>>>>
    >> (Jeroen?)).  >>>>> Debug builds for each revision
are
    >> available from >>>>> https://r-devel.github.io . To
    >> download the installer you need to >>>>> click the
github
    >> icon in the last column in the table. You need to be
    >> >>>>> signed in with a (free) Github account in
order to
    >> download builds >>>>> (artifacts) from Github
actions. It
    >> will show download links for both >>>>> the regular
    >> installer and installer with debug symbols.
    >> >>>>>
    >> >>>>> In other news, the https://r-devel.github.io
table
    >> also shows that the >>>>> fix that martin committed
is
    >> segfaulting on 32-bit.  >>>> Sorry that was inaccurate,
    >> it is not segfaulting at all, but the unit >>>> test is
    >> raising an error on 32-bit.
    >> >>
    >> 




    > ------------------------------

    > Message: 28 Date: Wed, 9 Sep 2020 10:53:18 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh
    > Parsonage <hugh.parsonage at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <6b01fb27-ec83-4dea-6478-c344f285083b at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > Thanks. Should be now fixed in 79169.  Tomas

    > On 9/9/20 10:32 AM, Hugh Parsonage wrote:
    >> R Under development (unstable) (2020-09-08 r79165)
    >> 
    >> On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote:
    >>> On 9/9/20 9:30 AM, Hugh Parsonage wrote:
    >>>> Thank you!
    >>>> 
    >>>> I get
    >>>> 
    >>>> Starting program:
    >>>> C:\R\R-devel-20200909\bin\x64\Rgui.exe [New Thread
    >>>> 19940.0x638c] [New Thread 19940.0x102c] [New Thread
    >>>> 19940.0x329c] [New Thread 19940.0x37dc] warning:
    >>>> Invalid parameter passed to C runtime function.
    >>>> 
    >>>> Program received signal SIGSEGV, Segmentation fault.
    >>>> 0x000000006c72d206 in compact_intseq_Dataptr
    >>>> (x=0x12783350, writeable=<optimized out>) at
    >>>> altclasses.c:169 169 altclasses.c: No such file or
    >>>> directory.
    >>> Thanks, would you know which svn version this is?
    >>> 
    >>> Tomas
    >>> 
    >>>> On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    >>>> <tomas.kalibera at gmail.com> wrote:
    >>>>> On 9/9/20 8:48 AM, Hugh Parsonage
wrote:>>>>> I am unable to set break or use gdb with any success when    >>>>> I use that version.
    >>>>>> >>>>> On linux I would do R -d gdb but this gives "unknown
    >>>>>> option '-d' ">>>>> while gdb R.exe (in the same directory as the debug
    >>>>>> version) gives the>>>>> same output as before.
    >>>>>> >>>>> I'm happy to help but I appreciate this list might not
be
    >>>>>> the best>>>>> place to get a tutorial on using gdb on Windows.    >>>>> Essentially, the steps are: build with DEBUG=T (to
    >>>>> have debug symbols), possibly updating EOPTS in
    >>>>> MkRules.local to disable optimizations, then run gdb
    >>>>> loading RGui, "set solib-search-path", run
RGui from
    >>>>> gdb. Then you can break to debugger from RGui menu, or
    >>>>> just run the code that segfaults, and you get to gdb
    >>>>> and can print the stacktrace, etc. You can find some
    >>>>> information in rw-FAQ (R for Windows FAQ), but yes, it
    >>>>> is harder than on Linux. We can take care of this
    >>>>> report, but of course in the longer term it would help
    >>>>> if more people could take their time to setup
    >>>>> debugging and analyze bugs even on Windows.
    >>>>> 
    >>>>> Tomas
    >>>>> >>>>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms    >>>>> <jeroenooms at gmail.com> wrote:
    >>>>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >>>>>>> <jeroenooms at gmail.com> wrote:
    >>>>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas
Kalibera
    >>>>>>>> <tomas.kalibera at gmail.com> wrote:
    >>>>>>>>> On 9/8/20 4:48 PM, Hugh Parsonage
wrote:
    >>>>>>>>>> Unfortunately I only get
    >>>>>>>>>> 
    >>>>>>>>>> [Thread 21752.0x4aa8 exited with
code 3221225477]
    >>>>>>>>>> [Thread 21752.0x4514 exited with
code 3221225477]
    >>>>>>>>>> [Thread 21752.0x3f10 exited with
code 3221225477]
    >>>>>>>>>> [Inferior 1 (process 21752) exited
with code
    >>>>>>>>>> 030000000005]
    >>>>>>>>>> 
    >>>>>>>>>> (I'm guessing I would need to
build an
    >>>>>>>>>> instrumented version of R, or can R
be debugged
    >>>>>>>>>> using gdb with an off-the-shelf
installation?)
    >>>>>>>>> No, the default build lacks debug
symbols. You
    >>>>>>>>> need a build with debug symbols, and if
you can
    >>>>>>>>> reproduce in a build without compiler
    >>>>>>>>> optimizations (-O0), the backtrace may
be easier
    >>>>>>>>> to interpret. Some bugs however
"disappear" when
    >>>>>>>>> optimizations are disabled. You can
build R from
    >>>>>>>>> source (and there may be debug builds
provided by
    >>>>>>>>> someone else (Jeroen?)).
    >>>>>>>> Debug builds for each revision are
available from
    >>>>>>>> https://r-devel.github.io . To download the
    >>>>>>>> installer you need to click the github icon
in the
    >>>>>>>> last column in the table. You need to be
signed in
    >>>>>>>> with a (free) Github account in order to
download
    >>>>>>>> builds (artifacts) from Github actions. It
will
    >>>>>>>> show download links for both the regular
installer
    >>>>>>>> and installer with debug symbols.
    >>>>>>>> 
    >>>>>>>> In other news, the
https://r-devel.github.io table
    >>>>>>>> also shows that the fix that martin
committed is
    >>>>>>>> segfaulting on 32-bit.
    >>>>>>> Sorry that was inaccurate, it is not
segfaulting at
    >>>>>>> all, but the unit test is raising an error on
    >>>>>>> 32-bit.




    > ------------------------------

    > Message: 29 Date: Wed, 9 Sep 2020 11:06:12 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Jeroen Ooms
    > <jeroenooms at gmail.com> Cc: Hugh Parsonage
    > <hugh.parsonage at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <5fd517e2-ad46-c343-2a63-cda01ff58acc at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > On 9/8/20 11:47 PM, Jeroen Ooms wrote:
    >> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote:
    >>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >>> <tomas.kalibera at gmail.com> wrote:
    >>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
    >>>>> Unfortunately I only get
    >>>>> 
    >>>>> [Thread 21752.0x4aa8 exited with code 3221225477]
    >>>>> [Thread 21752.0x4514 exited with code 3221225477]
    >>>>> [Thread 21752.0x3f10 exited with code 3221225477]
    >>>>> [Inferior 1 (process 21752) exited with code
    >>>>> 030000000005]
    >>>>> 
    >>>>> (I'm guessing I would need to build an instrumented
    >>>>> version of R, or can R be debugged using gdb with an
    >>>>> off-the-shelf installation?)
    >>>> No, the default build lacks debug symbols. You need a
    >>>> build with debug symbols, and if you can reproduce in a
    >>>> build without compiler optimizations (-O0), the
    >>>> backtrace may be easier to interpret. Some bugs however
    >>>> "disappear" when optimizations are disabled. You
can
    >>>> build R from source (and there may be debug builds
    >>>> provided by someone else (Jeroen?)).
    >>> Debug builds for each revision are available from
    >>> https://r-devel.github.io . To download the installer
    >>> you need to click the github icon in the last column in
    >>> the table. You need to be signed in with a (free) Github
    >>> account in order to download builds (artifacts) from
    >>> Github actions. It will show download links for both the
    >>> regular installer and installer with debug symbols.
    >>> 
    >>> In other news, the https://r-devel.github.io table also
    >>> shows that the fix that martin committed is segfaulting
    >>> on 32-bit.
    >> Sorry that was inaccurate, it is not segfaulting at all,
    >> but the unit test is raising an error on 32-bit.

    > Now fixed, the test needs to be run only on 64-bit builds
    > where such long vectors/sequences are allowed.

    > Tomas




    > ------------------------------

    > Subject: Digest Footer

    > _______________________________________________
    > R-devel at r-project.org mailing list DIGESTED
    > https://stat.ethz.ch/mailman/listinfo/r-devel


    > ------------------------------

    > End of R-devel Digest, Vol 211, Issue 7
    > ***************************************
    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

Abby Spurdle

2020-Sep-11 02:02 UTC

head link

[Rd] more Matrix weirdness

>     > "These operators are also implicit S4 generics, but as
>     > primitives, S4 methods will be dispatched only on S4
>     > objects ?x?."
> Yes, exactly,  very well found, Georgi!
I'm sorry Martin, but I don't understand your point here.

I'm assuming that you want the (S3) matrix, x, to be converted to an
(S4) Matrix.

However, this is not a question of method dispatch, as such.
But rather a question of type conversion (integer to numeric to complex, etc).

Specifically, can/should automatic type conversion, convert an S3 data
type to an S4 data type, even where user-defined data types are
involved?

Georgi Boshnakov

2020-Sep-11 09:06 UTC

head link

[Rd] more Matrix weirdness

If the current semantics is to be kept, one approach might be to insert in the
internal code of "[<-" something like the equivalent of

If(isS4(value))
    value <- coreData(value)

with the contract that classes that wish to be treated as equivalent to basic
vector classes define suitable method for coreData(). So, a matrix class would
return a plain matrix, a vector class - a vector, etc. This is akin to
coredata() for time series in package 'zoo' and others.


Georgi Boshnakov

-----Original Message-----
From: Martin Maechler <maechler at stat.math.ethz.ch> 
Sent: 10 September 2020 13:48
To: Georgi Boshnakov <georgi.boshnakov at manchester.ac.uk>
Cc: r-devel at r-project.org
Subject: Re: [Rd] more Matrix weirdness
>>>>> Georgi Boshnakov 
>>>>>     on Wed, 9 Sep 2020 10:48:56 +0000 writes:
    > I think that this is because `[<-` dispatches on S4
    > methods only if the first argument is S4.  ?"[<-" says:

    > "These operators are also implicit S4 generics, but as
    > primitives, S4 methods will be dispatched only on S4
    > objects ?x?."

    > Georgi Boshnakov

Yes, exactly,  very well found, Georgi!

This is something I would have wanted different for years, exactly because of
several such problems with the Matrix package of which I'm the maintainer.

Long time ago I had also looked if I saw how to fix this behavior inside
'methods' (i.e. the S4 infrastructure pkg) and I think in this case
also, inside R's basic C code.

At the time (~ 10 yrs ago) I gave up, but don't remember why.

I'm happy if you create a formal bug report, possibly "wishlist"
as it is documented behavior, for this infelicity...
and then I will probably add the  'HELPWANTED'  keyword.

Martin


    > -----Original Message-----


    > Message: 19 Date: Tue, 8 Sep 2020 22:04:44 -0400 From: Ben
    > Bolker <bbolker at gmail.com> To: r-devel
    > <r-devel at r-project.org> Subject: [Rd] more Matrix
    > weirdness Message-ID:
    > <fbaf45b7-b6d8-e93f-39d9-aa51d6f2c28e at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    >    Am I being too optimistic in expecting this (mixing and
    > matching matrices and Matrices) to work?  If x is a matrix
    > and m is a Matrix, replacing a commensurately sized
    > sub-matrix of x with m throws "number of items to replace
    > is not a multiple of replacement length" ...

    > x <- matrix(0,nrow=3,ncol=10,
    > dimnames=list(letters[1:3],LETTERS[1:10])) rr <-
    > c("a","b","c") cc <-
c("B","C","E") m <-
    > Matrix(matrix(1:9,3,3)) x[rr,cc] <- m

    >     cheers Ben Bolker




    > ------------------------------

    > Message: 20 Date: Wed, 9 Sep 2020 07:03:47 +0100 From: Rui
    > Barradas <ruipbarradas at sapo.pt> To: Ben Bolker
    > <bbolker at gmail.com>, r-devel <r-devel at r-project.org>
    > Subject: Re: [Rd] more Matrix weirdness Message-ID:
    > <7037975c-22b6-6eca-d871-743eead534f2 at sapo.pt>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > Hello,

    > R 4.0.2 on Ubuntu 20.04, sessionInfo() below.

    > I can reproduce this, sort of. The error I'm getting is
    > different:


    > x[rr, cc] <- m #Error in x[rr, cc] <- m : replacement has
    > length zero

    > But if I check lengths and dimensions, they are
    > identical().

    > identical(length(x[rr, cc]), length(m)) #[1] TRUE
    > identical(dim(x[rr, cc]), dim(m)) #[1] TRUE


    > What works is


    > x[rr, cc] <- as.matrix(m)

    > I ran Ben's code on RStudio 1.3.1073, the following is run
    > with Rscript and the error message is the same.


    > rui at rui:~$ Rscript --vanilla rhelp.R R version 4.0.2
    > (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit)
    > Running under: Ubuntu 20.04.1 LTS

    > Matrix products: default BLAS:
    > /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK:
    > /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

    > locale: [1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C [3]
    > LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8 [5]
    > LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8 [7]
    > LC_PAPER=pt_PT.UTF-8 LC_NAME=C [9] LC_ADDRESS=C
    > LC_TELEPHONE=C [11] LC_MEASUREMENT=pt_PT.UTF-8
    > LC_IDENTIFICATION=C

    > attached base packages: [1] stats graphics grDevices utils
    > datasets methods base

    > other attached packages: [1] Matrix_1.2-18

    > loaded via a namespace (and not attached): [1]
    > compiler_4.0.2 grid_4.0.2 lattice_0.20-41 Error in x[rr,
    > cc] <- m : number of items to replace is not a multiple of
    > replacement length Execution halted


    > Hope this helps,

    > Rui Barradas


    > ?s 03:04 de 09/09/20, Ben Bolker escreveu:
    >> ? Am I being too optimistic in expecting this (mixing and
    >> matching matrices and Matrices) to work?? If x is a
    >> matrix and m is a Matrix, replacing a commensurately
    >> sized sub-matrix of x with m throws "number of items to
    >> replace is not a multiple of replacement length" ...
    >> 
    >> x <- matrix(0,nrow=3,ncol=10,
    >> dimnames=list(letters[1:3],LETTERS[1:10])) rr <-
    >> c("a","b","c") cc <-
c("B","C","E") m <-
    >> Matrix(matrix(1:9,3,3)) x[rr,cc] <- m
    >> 
    >> ?? cheers ??? Ben Bolker
    >> 
    >> ______________________________________________
    >> R-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel




    > ------------------------------

    > Message: 21 Date: Wed, 9 Sep 2020 08:27:06 +0200 From: Uwe
    > Ligges <ligges at statistik.tu-dortmund.de> To:
    > r-devel at r-project.org Subject: Re: [Rd] failing automatic
    > incoming check Message-ID:
    > <fba137f3-e4c4-316e-47ae-ee11b08bc0c2 at
statistik.tu-dortmund.de>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"



    > On 08.09.2020 21:34, Sebastian P. Luque wrote:
    >> Hello,
    >> 
    >> I got a notification regarding a failure to pass incoming
    >> checks automatically after a CRAN submission.  The
    >> details are given here:
    >> 
    >>
https://win-builder.r-project.org/incoming_pretest/diveMove_1.5.0_20200908_191325/
    >> 
    >> The only visible issue is a NOTE from the macosx build,
    >> with the very terse:
    >> 
    >> "No Protocol Specified"
    >> 
    >> My searches suggest this can be ignored, but it would be
    >> nice to squash it.  Any tips welcome.
    >> 


    > For some reason this should hgave undergone manual
    > inpection but got auto rejected. Ideally you would reduce
    > the test timing so that the overall check time is less
    > than 10 min .

    > Best, Uwe Ligges




    > ------------------------------

    > Message: 22 Date: Wed, 9 Sep 2020 16:48:40 +1000 From:
    > Hugh Parsonage <hugh.parsonage at gmail.com> To: Jeroen Ooms
    > <jeroenooms at gmail.com> Cc: Tomas Kalibera
    > <tomas.kalibera at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <CAJmOi+PZcdsLRiBca2_r3dj0RmAJcuFT9FCjkMBjJEdFQ98YTQ at
mail.gmail.com>
    > Content-Type: text/plain; charset="utf-8"

    > I am unable to set break or use gdb with any success when
    > I use that version.

    > On linux I would do R -d gdb but this gives "unknown
    > option '-d' " while gdb R.exe (in the same directory as
    > the debug version) gives the same output as before.

    > I'm happy to help but I appreciate this list might not be
    > the best place to get a tutorial on using gdb on Windows.

    > On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    > <jeroenooms at gmail.com> wrote:
    >> 
    >> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote:
    >> >
    >> > On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote:
    >> > >
    >> > > On 9/8/20 4:48 PM, Hugh Parsonage wrote: > > >
    >> Unfortunately I only get
    >> > > >
    >> > > > [Thread 21752.0x4aa8 exited with code 3221225477]
>
    >> > > [Thread 21752.0x4514 exited with code 3221225477] >
>
    >> > [Thread 21752.0x3f10 exited with code 3221225477] > >
>
    >> [Inferior 1 (process 21752) exited with code
    >> 030000000005]
    >> > > >
    >> > > > (I'm guessing I would need to build an
instrumented
    >> version of R, or > > > can R be debugged using gdb with
    >> an off-the-shelf installation?)
    >> > >
    >> > > No, the default build lacks debug symbols. You need a
    >> build with debug > > symbols, and if you can reproduce in
    >> a build without compiler > > optimizations (-O0), the
    >> backtrace may be easier to interpret. Some bugs > >
    >> however "disappear" when optimizations are disabled. You
    >> can build R > > from source (and there may be debug
    >> builds provided by someone else > > (Jeroen?)).
    >> >
    >> > Debug builds for each revision are available from >
    >> https://r-devel.github.io . To download the installer you
    >> need to > click the github icon in the last column in the
    >> table. You need to be > signed in with a (free) Github
    >> account in order to download builds > (artifacts) from
    >> Github actions. It will show download links for both >
    >> the regular installer and installer with debug symbols.
    >> >
    >> > In other news, the https://r-devel.github.io table also
    >> shows that the > fix that martin committed is segfaulting
    >> on 32-bit.
    >> 
    >> Sorry that was inaccurate, it is not segfaulting at all,
    >> but the unit test is raising an error on 32-bit.




    > ------------------------------

    > Message: 23 Date: Wed, 9 Sep 2020 09:03:05 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh
    > Parsonage <hugh.parsonage at gmail.com>, Jeroen Ooms
    > <jeroenooms at gmail.com> Cc: Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <3f8e27b4-c6ed-04fe-7878-66d07ddc673f at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > On 9/9/20 8:48 AM, Hugh Parsonage wrote:
    >> I am unable to set break or use gdb with any success when
    >> I use that version.
    >> 
    >> On linux I would do R -d gdb but this gives "unknown
    >> option '-d' " while gdb R.exe (in the same directory
as
    >> the debug version) gives the same output as before.
    >> 
    >> I'm happy to help but I appreciate this list might not be
    >> the best place to get a tutorial on using gdb on Windows.

    > Essentially, the steps are: build with DEBUG=T (to have
    > debug symbols), possibly updating EOPTS in MkRules.local
    > to disable optimizations, then run gdb loading RGui, "set
    > solib-search-path", run RGui from gdb. Then you can break
    > to debugger from RGui menu, or just run the code that
    > segfaults, and you get to gdb and can print the
    > stacktrace, etc. You can find some information in rw-FAQ
    > (R for Windows FAQ), but yes, it is harder than on
    > Linux. We can take care of this report, but of course in
    > the longer term it would help if more people could take
    > their time to setup debugging and analyze bugs even on
    > Windows.

    > Tomas

    >> 
    >> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote:
    >>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >>> <jeroenooms at gmail.com> wrote:
    >>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >>>> <tomas.kalibera at gmail.com> wrote:
    >>>>> On 9/8/20 4:48 PM, Hugh Parsonage
wrote:>>>>> Unfortunately I only get
    >>>>>> >>>>> [Thread 21752.0x4aa8 exited with code 3221225477] [Thread 
>>>>> 21752.0x4514 exited with code 3221225477] [Thread
21752.0x3f10
>>>>> exited with code 3221225477] [Inferior 1 (process 21752)
exited
>>>>> with code 030000000005]
    >>>>>> >>>>> (I'm guessing I would need to build an instrumented
    >>>>>> version of R, or>>>>> can R be debugged using gdb with an off-the-shelf    >>>>>> installation?)
    >>>>> No, the default build lacks debug symbols. You need a
    >>>>> build with debug symbols, and if you can reproduce in
    >>>>> a build without compiler optimizations (-O0), the
    >>>>> backtrace may be easier to interpret. Some bugs
    >>>>> however "disappear" when optimizations are
    >>>>> disabled. You can build R from source (and there may
    >>>>> be debug builds provided by someone else (Jeroen?)).
    >>>> Debug builds for each revision are available from
    >>>> https://r-devel.github.io . To download the installer
    >>>> you need to click the github icon in the last column in
    >>>> the table. You need to be signed in with a (free)
    >>>> Github account in order to download builds (artifacts)
    >>>> from Github actions. It will show download links for
    >>>> both the regular installer and installer with debug
    >>>> symbols.
    >>>> 
    >>>> In other news, the https://r-devel.github.io table also
    >>>> shows that the fix that martin committed is segfaulting
    >>>> on 32-bit.
    >>> Sorry that was inaccurate, it is not segfaulting at all,
    >>> but the unit test is raising an error on 32-bit.




    > ------------------------------

    > Message: 24 Date: Wed, 9 Sep 2020 17:30:17 +1000 From:
    > Hugh Parsonage <hugh.parsonage at gmail.com> To: Tomas
    > Kalibera <tomas.kalibera at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <CAJmOi+MKW_RbxvVOfPDA58aYPzNz8ViKsVa+30ERsjmsV5Je+A at
mail.gmail.com>
    > Content-Type: text/plain; charset="utf-8"

    > Thank you!

    > I get

    > Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
    > [New Thread 19940.0x638c] [New Thread 19940.0x102c] [New
    > Thread 19940.0x329c] [New Thread 19940.0x37dc] warning:
    > Invalid parameter passed to C runtime function.

    > Program received signal SIGSEGV, Segmentation fault.
    > 0x000000006c72d206 in compact_intseq_Dataptr
    > (x=0x12783350, writeable=<optimized out>) at
    > altclasses.c:169 169 altclasses.c: No such file or
    > directory.

    > On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    > <tomas.kalibera at gmail.com> wrote:
    >> 
    >> On 9/9/20 8:48 AM, Hugh Parsonage wrote: > I am unable to
    >> set break or use gdb with any success when I use that
    >> version.
    >> >
    >> > On linux I would do R -d gdb but this gives "unknown
    >> option '-d' " > while gdb R.exe (in the same
directory as
    >> the debug version) gives the > same output as before.
    >> >
    >> > I'm happy to help but I appreciate this list might not
    >> be the best > place to get a tutorial on using gdb on
    >> Windows.
    >> 
    >> Essentially, the steps are: build with DEBUG=T (to have
    >> debug symbols), possibly updating EOPTS in MkRules.local
    >> to disable optimizations, then run gdb loading RGui, "set
    >> solib-search-path", run RGui from gdb. Then you can break
    >> to debugger from RGui menu, or just run the code that
    >> segfaults, and you get to gdb and can print the
    >> stacktrace, etc. You can find some information in rw-FAQ
    >> (R for Windows FAQ), but yes, it is harder than on
    >> Linux. We can take care of this report, but of course in
    >> the longer term it would help if more people could take
    >> their time to setup debugging and analyze bugs even on
    >> Windows.
    >> 
    >> Tomas
    >> 
    >> >
    >> > On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote: >> On Tue, Sep 8, 2020
at
    >> 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote:
>>> On
    >> Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote: >>>> On
9/8/20 4:48 PM,
    >> Hugh Parsonage wrote: >>>>> Unfortunately I only get
    >> >>>>>
    >> >>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
    >> >>>>> [Thread 21752.0x4514 exited with code
3221225477]
    >> >>>>> [Thread 21752.0x3f10 exited with code
3221225477]
    >> >>>>> [Inferior 1 (process 21752) exited with code
    >> 030000000005]
    >> >>>>>
    >> >>>>> (I'm guessing I would need to build an
instrumented
    >> version of R, or >>>>> can R be debugged using gdb
with
    >> an off-the-shelf installation?)  >>>> No, the default
    >> build lacks debug symbols. You need a build with debug
    >> >>>> symbols, and if you can reproduce in a build
without
    >> compiler >>>> optimizations (-O0), the backtrace may be
    >> easier to interpret. Some bugs >>>> however
"disappear"
    >> when optimizations are disabled. You can build R >>>>
    >> from source (and there may be debug builds provided by
    >> someone else >>>> (Jeroen?)).  >>> Debug
builds for each
    >> revision are available from >>> https://r-devel.github.io
    >> . To download the installer you need to >>> click the
    >> github icon in the last column in the table. You need to
    >> be >>> signed in with a (free) Github account in order to
    >> download builds >>> (artifacts) from Github actions. It
    >> will show download links for both >>> the regular
    >> installer and installer with debug symbols.
    >> >>>
    >> >>> In other news, the https://r-devel.github.io table
    >> also shows that the >>> fix that martin committed is
    >> segfaulting on 32-bit.  >> Sorry that was inaccurate, it
    >> is not segfaulting at all, but the unit >> test is
    >> raising an error on 32-bit.
    >> 
    >> 




    > ------------------------------

    > Message: 25 Date: Wed, 9 Sep 2020 08:00:41 +0000 From:
    > "Koenker, Roger W" <rkoenker at illinois.edu> To:
r-devel
    > <r-devel at r-project.org> Subject: [Rd] Environmental
    > Messaging Message-ID:
    > <6C9F497D-5CEA-4A02-B7AB-490AB4022BB6 at illinois.edu>
    > Content-Type: text/plain; charset="utf-8"

    > What sort of message is this to send to the younger
    > generation?

    >> plastic = 1:5 card = 1:4 board = 1:4
    >> plastic/crossprod(card,board)
    > [1] 0.03333333 0.06666667 0.10000000 0.13333333 0.16666667
    > Warning message: In plastic/crossprod(card, board) :
    > Recycling array of length 1 in vector-array arithmetic is
    > deprecated.  Use c() or as.vector() instead.

    > ok, I can write c(crossprod()) but it is ugly, and
    > environmentally wasteful.  What?s next?  Warnings for my
    > beloved outer(card, board) * board

    > ------------------------------

    > Message: 26 Date: Wed, 9 Sep 2020 10:00:55 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh
    > Parsonage <hugh.parsonage at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <8383dabf-9093-41ea-2407-8bd75a1009e2 at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > On 9/9/20 9:30 AM, Hugh Parsonage wrote:
    >> Thank you!
    >> 
    >> I get
    >> 
    >> Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe
    >> [New Thread 19940.0x638c] [New Thread 19940.0x102c] [New
    >> Thread 19940.0x329c] [New Thread 19940.0x37dc] warning:
    >> Invalid parameter passed to C runtime function.
    >> 
    >> Program received signal SIGSEGV, Segmentation fault.
    >> 0x000000006c72d206 in compact_intseq_Dataptr
    >> (x=0x12783350, writeable=<optimized out>) at
    >> altclasses.c:169 169 altclasses.c: No such file or
    >> directory.

    > Thanks, would you know which svn version this is?

    > Tomas

    >> 
    >> On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote:
    >>> On 9/9/20 8:48 AM, Hugh Parsonage wrote:
    >>>> I am unable to set break or use gdb with any success
    >>>> when I use that version.
    >>>> 
    >>>> On linux I would do R -d gdb but this gives "unknown
    >>>> option '-d' " while gdb R.exe (in the same
directory as
    >>>> the debug version) gives the same output as before.
    >>>> 
    >>>> I'm happy to help but I appreciate this list might not
    >>>> be the best place to get a tutorial on using gdb on
    >>>> Windows.
    >>> Essentially, the steps are: build with DEBUG=T (to have
    >>> debug symbols), possibly updating EOPTS in MkRules.local
    >>> to disable optimizations, then run gdb loading RGui,
    >>> "set solib-search-path", run RGui from gdb. Then you
can
    >>> break to debugger from RGui menu, or just run the code
    >>> that segfaults, and you get to gdb and can print the
    >>> stacktrace, etc. You can find some information in rw-FAQ
    >>> (R for Windows FAQ), but yes, it is harder than on
    >>> Linux. We can take care of this report, but of course in
    >>> the longer term it would help if more people could take
    >>> their time to setup debugging and analyze bugs even on
    >>> Windows.
    >>> 
    >>> Tomas
    >>> 
    >>>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >>>> <jeroenooms at gmail.com> wrote:
    >>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >>>>> <jeroenooms at gmail.com>
wrote:>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera    >>>>> <tomas.kalibera at gmail.com> wrote:
    >>>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
    >>>>>>>> Unfortunately I only get
    >>>>>>>> 
    >>>>>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
    >>>>>>>> [Thread 21752.0x4514 exited with code
3221225477]
    >>>>>>>> [Thread 21752.0x3f10 exited with code
3221225477]
    >>>>>>>> [Inferior 1 (process 21752) exited with
code
    >>>>>>>> 030000000005]
    >>>>>>>> 
    >>>>>>>> (I'm guessing I would need to build an
instrumented
    >>>>>>>> version of R, or can R be debugged using
gdb with
    >>>>>>>> an off-the-shelf installation?)
    >>>>>>> No, the default build lacks debug symbols. You
need
    >>>>>>> a build with debug symbols, and if you can
reproduce
    >>>>>>> in a build without compiler optimizations
(-O0), the
    >>>>>>> backtrace may be easier to interpret. Some bugs
    >>>>>>> however "disappear" when
optimizations are
    >>>>>>> disabled. You can build R from source (and
there may
    >>>>>>> be debug builds provided by someone else
(Jeroen?)).>>>>> Debug builds for each revision are available from 
>>>>> https://r-devel.github.io . To download the installer you
    >>>>>>> need to>>>>> click the github icon in the last column in the table. You
    >>>>>>> need to be>>>>> signed in with a (free) Github account in order to
    >>>>>>> download builds>>>>> (artifacts) from Github actions. It will show download
    >>>>>>> links for both>>>>> the regular installer and installer with debug symbols.
    >>>>>> >>>>> In other news, the https://r-devel.github.io table also
    >>>>>> shows that the>>>>> fix that martin committed is segfaulting on 32-bit.    >>>>> Sorry that was inaccurate, it is not segfaulting at
    >>>>> all, but the unit test is raising an error on 32-bit.
    >>> 




    > ------------------------------

    > Message: 27 Date: Wed, 9 Sep 2020 18:32:58 +1000 From:
    > Hugh Parsonage <hugh.parsonage at gmail.com> To: Tomas
    > Kalibera <tomas.kalibera at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <CAJmOi+MLyn_WcBLFSQdL9ze4iDzazysPcU7QGOQtWryTod44Yg at
mail.gmail.com>
    > Content-Type: text/plain; charset="utf-8"

    > R Under development (unstable) (2020-09-08 r79165)

    > On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera
    > <tomas.kalibera at gmail.com> wrote:
    >> 
    >> On 9/9/20 9:30 AM, Hugh Parsonage wrote: > Thank you!
    >> >
    >> > I get
    >> >
    >> > Starting program:
    >> C:\R\R-devel-20200909\bin\x64\Rgui.exe > [New Thread
    >> 19940.0x638c] > [New Thread 19940.0x102c] > [New Thread
    >> 19940.0x329c] > [New Thread 19940.0x37dc] > warning:
    >> Invalid parameter passed to C runtime function.
    >> >
    >> > Program received signal SIGSEGV, Segmentation fault.  >
    >> 0x000000006c72d206 in compact_intseq_Dataptr
    >> (x=0x12783350, > writeable=<optimized out>) at
    >> altclasses.c:169 > 169 altclasses.c: No such file or
    >> directory.
    >> 
    >> Thanks, would you know which svn version this is?
    >> 
    >> Tomas
    >> 
    >> >
    >> > On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote: >> On 9/9/20 8:48
AM,
    >> Hugh Parsonage wrote: >>> I am unable to set break or use
    >> gdb with any success when I use that version.
    >> >>>
    >> >>> On linux I would do R -d gdb but this gives
"unknown
    >> option '-d' " >>> while gdb R.exe (in the
same directory
    >> as the debug version) gives the >>> same output as
    >> before.
    >> >>>
    >> >>> I'm happy to help but I appreciate this list might
    >> not be the best >>> place to get a tutorial on using gdb
    >> on Windows.  >> Essentially, the steps are: build with
    >> DEBUG=T (to have debug symbols), >> possibly updating
    >> EOPTS in MkRules.local to disable optimizations, then >>
    >> run gdb loading RGui, "set solib-search-path", run RGui
    >> from gdb. Then >> you can break to debugger from RGui
    >> menu, or just run the code that >> segfaults, and you get
    >> to gdb and can print the stacktrace, etc. You can >> find
    >> some information in rw-FAQ (R for Windows FAQ), but yes,
    >> it is >> harder than on Linux. We can take care of this
    >> report, but of course in >> the longer term it would help
    >> if more people could take their time to >> setup
    >> debugging and analyze bugs even on Windows.
    >> >>
    >> >> Tomas
    >> >>
    >> >>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote: >>>> On Tue, Sep
8, 2020 at
    >> 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote:
>>>>>
    >> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote: >>>>>>
On 9/8/20 4:48
    >> PM, Hugh Parsonage wrote: >>>>>>>
Unfortunately I only
    >> get
    >> >>>>>>>
    >> >>>>>>> [Thread 21752.0x4aa8 exited with code
3221225477]
    >> >>>>>>> [Thread 21752.0x4514 exited with code
3221225477]
    >> >>>>>>> [Thread 21752.0x3f10 exited with code
3221225477]
    >> >>>>>>> [Inferior 1 (process 21752) exited
with code
    >> 030000000005]
    >> >>>>>>>
    >> >>>>>>> (I'm guessing I would need to
build an
    >> instrumented version of R, or >>>>>>> can R be
debugged
    >> using gdb with an off-the-shelf installation?) 
>>>>>>
    >> No, the default build lacks debug symbols. You need a
    >> build with debug >>>>>> symbols, and if you can
reproduce
    >> in a build without compiler >>>>>> optimizations
(-O0),
    >> the backtrace may be easier to interpret. Some bugs
    >> >>>>>> however "disappear" when
optimizations are
    >> disabled. You can build R >>>>>> from source (and
there
    >> may be debug builds provided by someone else
>>>>>>
    >> (Jeroen?)).  >>>>> Debug builds for each revision
are
    >> available from >>>>> https://r-devel.github.io . To
    >> download the installer you need to >>>>> click the
github
    >> icon in the last column in the table. You need to be
    >> >>>>> signed in with a (free) Github account in
order to
    >> download builds >>>>> (artifacts) from Github
actions. It
    >> will show download links for both >>>>> the regular
    >> installer and installer with debug symbols.
    >> >>>>>
    >> >>>>> In other news, the https://r-devel.github.io
table
    >> also shows that the >>>>> fix that martin committed
is
    >> segfaulting on 32-bit.  >>>> Sorry that was inaccurate,
    >> it is not segfaulting at all, but the unit >>>> test is
    >> raising an error on 32-bit.
    >> >>
    >> 




    > ------------------------------

    > Message: 28 Date: Wed, 9 Sep 2020 10:53:18 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh
    > Parsonage <hugh.parsonage at gmail.com> Cc: Jeroen Ooms
    > <jeroenooms at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <6b01fb27-ec83-4dea-6478-c344f285083b at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > Thanks. Should be now fixed in 79169.  Tomas

    > On 9/9/20 10:32 AM, Hugh Parsonage wrote:
    >> R Under development (unstable) (2020-09-08 r79165)
    >> 
    >> On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera
    >> <tomas.kalibera at gmail.com> wrote:
    >>> On 9/9/20 9:30 AM, Hugh Parsonage wrote:
    >>>> Thank you!
    >>>> 
    >>>> I get
    >>>> 
    >>>> Starting program:
    >>>> C:\R\R-devel-20200909\bin\x64\Rgui.exe [New Thread
    >>>> 19940.0x638c] [New Thread 19940.0x102c] [New Thread
    >>>> 19940.0x329c] [New Thread 19940.0x37dc] warning:
    >>>> Invalid parameter passed to C runtime function.
    >>>> 
    >>>> Program received signal SIGSEGV, Segmentation fault.
    >>>> 0x000000006c72d206 in compact_intseq_Dataptr
    >>>> (x=0x12783350, writeable=<optimized out>) at
    >>>> altclasses.c:169 169 altclasses.c: No such file or
    >>>> directory.
    >>> Thanks, would you know which svn version this is?
    >>> 
    >>> Tomas
    >>> 
    >>>> On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera
    >>>> <tomas.kalibera at gmail.com> wrote:
    >>>>> On 9/9/20 8:48 AM, Hugh Parsonage
wrote:>>>>> I am unable to set break or use gdb with any success when    >>>>> I use that version.
    >>>>>> >>>>> On linux I would do R -d gdb but this gives "unknown
    >>>>>> option '-d' ">>>>> while gdb R.exe (in the same directory as the debug
    >>>>>> version) gives the>>>>> same output as before.
    >>>>>> >>>>> I'm happy to help but I appreciate this list might not
be
    >>>>>> the best>>>>> place to get a tutorial on using gdb on Windows.    >>>>> Essentially, the steps are: build with DEBUG=T (to
    >>>>> have debug symbols), possibly updating EOPTS in
    >>>>> MkRules.local to disable optimizations, then run gdb
    >>>>> loading RGui, "set solib-search-path", run
RGui from
    >>>>> gdb. Then you can break to debugger from RGui menu, or
    >>>>> just run the code that segfaults, and you get to gdb
    >>>>> and can print the stacktrace, etc. You can find some
    >>>>> information in rw-FAQ (R for Windows FAQ), but yes, it
    >>>>> is harder than on Linux. We can take care of this
    >>>>> report, but of course in the longer term it would help
    >>>>> if more people could take their time to setup
    >>>>> debugging and analyze bugs even on Windows.
    >>>>> 
    >>>>> Tomas
    >>>>> >>>>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms    >>>>> <jeroenooms at gmail.com> wrote:
    >>>>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >>>>>>> <jeroenooms at gmail.com> wrote:
    >>>>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas
Kalibera
    >>>>>>>> <tomas.kalibera at gmail.com> wrote:
    >>>>>>>>> On 9/8/20 4:48 PM, Hugh Parsonage
wrote:
    >>>>>>>>>> Unfortunately I only get
    >>>>>>>>>> 
    >>>>>>>>>> [Thread 21752.0x4aa8 exited with
code 3221225477]
    >>>>>>>>>> [Thread 21752.0x4514 exited with
code 3221225477]
    >>>>>>>>>> [Thread 21752.0x3f10 exited with
code 3221225477]
    >>>>>>>>>> [Inferior 1 (process 21752) exited
with code
    >>>>>>>>>> 030000000005]
    >>>>>>>>>> 
    >>>>>>>>>> (I'm guessing I would need to
build an
    >>>>>>>>>> instrumented version of R, or can R
be debugged
    >>>>>>>>>> using gdb with an off-the-shelf
installation?)
    >>>>>>>>> No, the default build lacks debug
symbols. You
    >>>>>>>>> need a build with debug symbols, and if
you can
    >>>>>>>>> reproduce in a build without compiler
    >>>>>>>>> optimizations (-O0), the backtrace may
be easier
    >>>>>>>>> to interpret. Some bugs however
"disappear" when
    >>>>>>>>> optimizations are disabled. You can
build R from
    >>>>>>>>> source (and there may be debug builds
provided by
    >>>>>>>>> someone else (Jeroen?)).
    >>>>>>>> Debug builds for each revision are
available from
    >>>>>>>> https://r-devel.github.io . To download the
    >>>>>>>> installer you need to click the github icon
in the
    >>>>>>>> last column in the table. You need to be
signed in
    >>>>>>>> with a (free) Github account in order to
download
    >>>>>>>> builds (artifacts) from Github actions. It
will
    >>>>>>>> show download links for both the regular
installer
    >>>>>>>> and installer with debug symbols.
    >>>>>>>> 
    >>>>>>>> In other news, the
https://r-devel.github.io table
    >>>>>>>> also shows that the fix that martin
committed is
    >>>>>>>> segfaulting on 32-bit.
    >>>>>>> Sorry that was inaccurate, it is not
segfaulting at
    >>>>>>> all, but the unit test is raising an error on
    >>>>>>> 32-bit.




    > ------------------------------

    > Message: 29 Date: Wed, 9 Sep 2020 11:06:12 +0200 From:
    > Tomas Kalibera <tomas.kalibera at gmail.com> To: Jeroen Ooms
    > <jeroenooms at gmail.com> Cc: Hugh Parsonage
    > <hugh.parsonage at gmail.com>, Luke Tierney
    > <luke-tierney at uiowa.edu>, R-devel <r-devel at
r-project.org>,
    > Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re:
    > [Rd] [External] Re: Operations with long altrep vectors
    > cause segfaults on Windows Message-ID:
    > <5fd517e2-ad46-c343-2a63-cda01ff58acc at gmail.com>
    > Content-Type: text/plain; charset="utf-8";
Format="flowed"

    > On 9/8/20 11:47 PM, Jeroen Ooms wrote:
    >> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
    >> <jeroenooms at gmail.com> wrote:
    >>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
    >>> <tomas.kalibera at gmail.com> wrote:
    >>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote:
    >>>>> Unfortunately I only get
    >>>>> 
    >>>>> [Thread 21752.0x4aa8 exited with code 3221225477]
    >>>>> [Thread 21752.0x4514 exited with code 3221225477]
    >>>>> [Thread 21752.0x3f10 exited with code 3221225477]
    >>>>> [Inferior 1 (process 21752) exited with code
    >>>>> 030000000005]
    >>>>> 
    >>>>> (I'm guessing I would need to build an instrumented
    >>>>> version of R, or can R be debugged using gdb with an
    >>>>> off-the-shelf installation?)
    >>>> No, the default build lacks debug symbols. You need a
    >>>> build with debug symbols, and if you can reproduce in a
    >>>> build without compiler optimizations (-O0), the
    >>>> backtrace may be easier to interpret. Some bugs however
    >>>> "disappear" when optimizations are disabled. You
can
    >>>> build R from source (and there may be debug builds
    >>>> provided by someone else (Jeroen?)).
    >>> Debug builds for each revision are available from
    >>> https://r-devel.github.io . To download the installer
    >>> you need to click the github icon in the last column in
    >>> the table. You need to be signed in with a (free) Github
    >>> account in order to download builds (artifacts) from
    >>> Github actions. It will show download links for both the
    >>> regular installer and installer with debug symbols.
    >>> 
    >>> In other news, the https://r-devel.github.io table also
    >>> shows that the fix that martin committed is segfaulting
    >>> on 32-bit.
    >> Sorry that was inaccurate, it is not segfaulting at all,
    >> but the unit test is raising an error on 32-bit.

    > Now fixed, the test needs to be run only on 64-bit builds
    > where such long vectors/sequences are allowed.

    > Tomas




    > ------------------------------

    > Subject: Digest Footer

    > _______________________________________________
    > R-devel at r-project.org mailing list DIGESTED
    > https://stat.ethz.ch/mailman/listinfo/r-devel


    > ------------------------------

    > End of R-devel Digest, Vol 211, Issue 7
    > ***************************************
    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

Reasonably Related Threads

Search for more seemingly similar threads

R devel - Sep 2020 - more Matrix weirdness

[Rd] more Matrix weirdness

[Rd] more Matrix weirdness

[Rd] more Matrix weirdness

[Rd] more Matrix weirdness

Reasonably Related Threads