[Rd] more Matrix weirdness
Georgi Boshnakov
georg|@bo@hn@kov @end|ng |rom m@nche@ter@@c@uk
Wed Sep 9 12:48:56 CEST 2020
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 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
------------------------------
Subject: Digest Footer
_______________________________________________
R-devel using r-project.org mailing list DIGESTED
https://stat.ethz.ch/mailman/listinfo/r-devel
------------------------------
End of R-devel Digest, Vol 211, Issue 7
***************************************
More information about the R-devel
mailing list