From georg|@bo@hn@kov @end|ng |rom m@nche@ter@@c@uk  Wed Sep  9 12:48:56 2020
From: georg|@bo@hn@kov @end|ng |rom m@nche@ter@@c@uk (Georgi Boshnakov)
Date: Wed, 9 Sep 2020 10:48:56 +0000
Subject: [Rd] more Matrix weirdness
Message-ID: <AM0PR0102MB3443F1F91F70197C52FE71ADAE260@AM0PR0102MB3443.eurprd01.prod.exchangelabs.com>

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




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[Rd] more Matrix weirdness
Georgi Boshnakov