[Rd] more Matrix weirdness
Georgi Boshnakov
georg|@bo@hn@kov @end|ng |rom m@nche@ter@@c@uk
Fri Sep 11 11:06:30 CEST 2020
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 using stat.math.ethz.ch>
Sent: 10 September 2020 13:48
To: Georgi Boshnakov <georgi.boshnakov using manchester.ac.uk>
Cc: r-devel using 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 using gmail.com> To: r-devel
> <r-devel using r-project.org> Subject: [Rd] more Matrix
> weirdness Message-ID:
> <fbaf45b7-b6d8-e93f-39d9-aa51d6f2c28e using 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 using sapo.pt> To: Ben Bolker
> <bbolker using gmail.com>, r-devel <r-devel using r-project.org>
> Subject: Re: [Rd] more Matrix weirdness Message-ID:
> <7037975c-22b6-6eca-d871-743eead534f2 using 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 using 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
> Às 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 using 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 using statistik.tu-dortmund.de> To:
> r-devel using r-project.org Subject: Re: [Rd] failing automatic
> incoming check Message-ID:
> <fba137f3-e4c4-316e-47ae-ee11b08bc0c2 using 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 using gmail.com> To: Jeroen Ooms
> <jeroenooms using gmail.com> Cc: Tomas Kalibera
> <tomas.kalibera using gmail.com>, Luke Tierney
> <luke-tierney using uiowa.edu>, R-devel <r-devel using r-project.org>,
> Martin Maechler <maechler using stat.math.ethz.ch> Subject: Re:
> [Rd] [External] Re: Operations with long altrep vectors
> cause segfaults on Windows Message-ID:
> <CAJmOi+PZcdsLRiBca2_r3dj0RmAJcuFT9FCjkMBjJEdFQ98YTQ using 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 using gmail.com> wrote:
>>
>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
>> <jeroenooms using gmail.com> wrote:
>> >
>> > On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
>> <tomas.kalibera using 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 using gmail.com> To: Hugh
> Parsonage <hugh.parsonage using gmail.com>, Jeroen Ooms
> <jeroenooms using gmail.com> Cc: Luke Tierney
> <luke-tierney using uiowa.edu>, R-devel <r-devel using r-project.org>,
> Martin Maechler <maechler using 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 using 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 using gmail.com> wrote:
>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
>>> <jeroenooms using gmail.com> wrote:
>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
>>>> <tomas.kalibera using 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 using gmail.com> To: Tomas
> Kalibera <tomas.kalibera using gmail.com> Cc: Jeroen Ooms
> <jeroenooms using gmail.com>, Luke Tierney
> <luke-tierney using uiowa.edu>, R-devel <r-devel using r-project.org>,
> Martin Maechler <maechler using 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 using 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 using 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 using gmail.com> wrote: >> On Tue, Sep 8, 2020 at
>> 11:44 PM Jeroen Ooms <jeroenooms using gmail.com> wrote: >>> On
>> Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
>> <tomas.kalibera using 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 using illinois.edu> To: r-devel
> <r-devel using r-project.org> Subject: [Rd] Environmental
> Messaging Message-ID:
> <6C9F497D-5CEA-4A02-B7AB-490AB4022BB6 using 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 using gmail.com> To: Hugh
> Parsonage <hugh.parsonage using gmail.com> Cc: Jeroen Ooms
> <jeroenooms using gmail.com>, Luke Tierney
> <luke-tierney using uiowa.edu>, R-devel <r-devel using r-project.org>,
> Martin Maechler <maechler using 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 using 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 using 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 using gmail.com> wrote:
>>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
>>>>> <jeroenooms using gmail.com> wrote:
>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
>>>>> <tomas.kalibera using 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 using gmail.com> To: Tomas
> Kalibera <tomas.kalibera using gmail.com> Cc: Jeroen Ooms
> <jeroenooms using gmail.com>, Luke Tierney
> <luke-tierney using uiowa.edu>, R-devel <r-devel using r-project.org>,
> Martin Maechler <maechler using stat.math.ethz.ch> Subject: Re:
> [Rd] [External] Re: Operations with long altrep vectors
> cause segfaults on Windows Message-ID:
> <CAJmOi+MLyn_WcBLFSQdL9ze4iDzazysPcU7QGOQtWryTod44Yg using 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 using 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 using 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 using gmail.com> wrote: >>>> On Tue, Sep 8, 2020 at
>> 11:44 PM Jeroen Ooms <jeroenooms using gmail.com> wrote: >>>>>
>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
>> <tomas.kalibera using 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 using gmail.com> To: Hugh
> Parsonage <hugh.parsonage using gmail.com> Cc: Jeroen Ooms
> <jeroenooms using gmail.com>, Luke Tierney
> <luke-tierney using uiowa.edu>, R-devel <r-devel using r-project.org>,
> Martin Maechler <maechler using 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 using 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 using 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 using 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 using gmail.com> wrote:
>>>>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms
>>>>>>> <jeroenooms using gmail.com> wrote:
>>>>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
>>>>>>>> <tomas.kalibera using 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 using gmail.com> To: Jeroen Ooms
> <jeroenooms using gmail.com> Cc: Hugh Parsonage
> <hugh.parsonage using gmail.com>, Luke Tierney
> <luke-tierney using uiowa.edu>, R-devel <r-devel using r-project.org>,
> Martin Maechler <maechler using 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 using 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 using gmail.com> wrote:
>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera
>>> <tomas.kalibera using 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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