From georg|@bo@hn@kov @end|ng |rom m@nche@ter@@c@uk  Fri Sep 11 11:06:30 2020
From: georg|@bo@hn@kov @end|ng |rom m@nche@ter@@c@uk (Georgi Boshnakov)
Date: Fri, 11 Sep 2020 09:06:30 +0000
Subject: [Rd] more Matrix weirdness
In-Reply-To: <24410.8333.102266.856181@stat.math.ethz.ch>
References: <AM0PR0102MB3443F1F91F70197C52FE71ADAE260@AM0PR0102MB3443.eurprd01.prod.exchangelabs.com>
 <24410.8333.102266.856181@stat.math.ethz.ch>
Message-ID: <AM0PR0102MB344377DD070F0B8BE8EAB65DAE240@AM0PR0102MB3443.eurprd01.prod.exchangelabs.com>

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


[Rd] more Matrix weirdness
Georgi Boshnakov