I think that this is because `[<-` dispatches on S4 methods only if the first argument is S4. ?"[<-" says: "These operators are also implicit S4 generics, but as primitives, S4 methods will be dispatched only on S4 objects ?x?." Georgi Boshnakov -----Original Message----- Message: 19 Date: Tue, 8 Sep 2020 22:04:44 -0400 From: Ben Bolker <bbolker at gmail.com> To: r-devel <r-devel at r-project.org> Subject: [Rd] more Matrix weirdness Message-ID: <fbaf45b7-b6d8-e93f-39d9-aa51d6f2c28e at gmail.com> Content-Type: text/plain; charset="utf-8"; Format="flowed" Am I being too optimistic in expecting this (mixing and matching matrices and Matrices) to work? If x is a matrix and m is a Matrix, replacing a commensurately sized sub-matrix of x with m throws "number of items to replace is not a multiple of replacement length" ... x <- matrix(0,nrow=3,ncol=10, dimnames=list(letters[1:3],LETTERS[1:10])) rr <- c("a","b","c") cc <- c("B","C","E") m <- Matrix(matrix(1:9,3,3)) x[rr,cc] <- m cheers Ben Bolker ------------------------------ Message: 20 Date: Wed, 9 Sep 2020 07:03:47 +0100 From: Rui Barradas <ruipbarradas at sapo.pt> To: Ben Bolker <bbolker at gmail.com>, r-devel <r-devel at r-project.org> Subject: Re: [Rd] more Matrix weirdness Message-ID: <7037975c-22b6-6eca-d871-743eead534f2 at sapo.pt> Content-Type: text/plain; charset="utf-8"; Format="flowed" Hello, R 4.0.2 on Ubuntu 20.04, sessionInfo() below. I can reproduce this, sort of. The error I'm getting is different: x[rr, cc] <- m #Error in x[rr, cc] <- m : replacement has length zero But if I check lengths and dimensions, they are identical(). identical(length(x[rr, cc]), length(m)) #[1] TRUE identical(dim(x[rr, cc]), dim(m)) #[1] TRUE What works is x[rr, cc] <- as.matrix(m) I ran Ben's code on RStudio 1.3.1073, the following is run with Rscript and the error message is the same. rui at rui:~$ Rscript --vanilla rhelp.R R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.1 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C [3] LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8 [5] LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8 [7] LC_PAPER=pt_PT.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Matrix_1.2-18 loaded via a namespace (and not attached): [1] compiler_4.0.2 grid_4.0.2 lattice_0.20-41 Error in x[rr, cc] <- m : number of items to replace is not a multiple of replacement length Execution halted Hope this helps, Rui Barradas ?s 03:04 de 09/09/20, Ben Bolker escreveu:> ? Am I being too optimistic in expecting this (mixing and matching > matrices and Matrices) to work?? If x is a matrix and m is a Matrix, > replacing a commensurately sized sub-matrix of x with m throws "number > of items to replace is not a multiple of replacement length" ... > > x <- matrix(0,nrow=3,ncol=10, dimnames=list(letters[1:3],LETTERS[1:10])) > rr <- c("a","b","c") > cc <- c("B","C","E") > m <- Matrix(matrix(1:9,3,3)) > x[rr,cc] <- m > > ?? cheers > ??? Ben Bolker > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel------------------------------ Message: 21 Date: Wed, 9 Sep 2020 08:27:06 +0200 From: Uwe Ligges <ligges at statistik.tu-dortmund.de> To: r-devel at r-project.org Subject: Re: [Rd] failing automatic incoming check Message-ID: <fba137f3-e4c4-316e-47ae-ee11b08bc0c2 at statistik.tu-dortmund.de> Content-Type: text/plain; charset="utf-8"; Format="flowed" On 08.09.2020 21:34, Sebastian P. Luque wrote:> Hello, > > I got a notification regarding a failure to pass incoming checks > automatically after a CRAN submission. The details are given here: > > https://win-builder.r-project.org/incoming_pretest/diveMove_1.5.0_20200908_191325/ > > The only visible issue is a NOTE from the macosx build, with the very > terse: > > "No Protocol Specified" > > My searches suggest this can be ignored, but it would be nice to squash > it. Any tips welcome. >For some reason this should hgave undergone manual inpection but got auto rejected. Ideally you would reduce the test timing so that the overall check time is less than 10 min . Best, Uwe Ligges ------------------------------ Message: 22 Date: Wed, 9 Sep 2020 16:48:40 +1000 From: Hugh Parsonage <hugh.parsonage at gmail.com> To: Jeroen Ooms <jeroenooms at gmail.com> Cc: Tomas Kalibera <tomas.kalibera at gmail.com>, Luke Tierney <luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>, Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re: [Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows Message-ID: <CAJmOi+PZcdsLRiBca2_r3dj0RmAJcuFT9FCjkMBjJEdFQ98YTQ at mail.gmail.com> Content-Type: text/plain; charset="utf-8" I am unable to set break or use gdb with any success when I use that version. On linux I would do R -d gdb but this gives "unknown option '-d' " while gdb R.exe (in the same directory as the debug version) gives the same output as before. I'm happy to help but I appreciate this list might not be the best place to get a tutorial on using gdb on Windows. On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com> wrote:> > On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote: > > > > On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > > > > > > On 9/8/20 4:48 PM, Hugh Parsonage wrote: > > > > Unfortunately I only get > > > > > > > > [Thread 21752.0x4aa8 exited with code 3221225477] > > > > [Thread 21752.0x4514 exited with code 3221225477] > > > > [Thread 21752.0x3f10 exited with code 3221225477] > > > > [Inferior 1 (process 21752) exited with code 030000000005] > > > > > > > > (I'm guessing I would need to build an instrumented version of R, or > > > > can R be debugged using gdb with an off-the-shelf installation?) > > > > > > No, the default build lacks debug symbols. You need a build with debug > > > symbols, and if you can reproduce in a build without compiler > > > optimizations (-O0), the backtrace may be easier to interpret. Some bugs > > > however "disappear" when optimizations are disabled. You can build R > > > from source (and there may be debug builds provided by someone else > > > (Jeroen?)). > > > > Debug builds for each revision are available from > > https://r-devel.github.io . To download the installer you need to > > click the github icon in the last column in the table. You need to be > > signed in with a (free) Github account in order to download builds > > (artifacts) from Github actions. It will show download links for both > > the regular installer and installer with debug symbols. > > > > In other news, the https://r-devel.github.io table also shows that the > > fix that martin committed is segfaulting on 32-bit. > > Sorry that was inaccurate, it is not segfaulting at all, but the unit > test is raising an error on 32-bit.------------------------------ Message: 23 Date: Wed, 9 Sep 2020 09:03:05 +0200 From: Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh Parsonage <hugh.parsonage at gmail.com>, Jeroen Ooms <jeroenooms at gmail.com> Cc: Luke Tierney <luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>, Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re: [Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows Message-ID: <3f8e27b4-c6ed-04fe-7878-66d07ddc673f at gmail.com> Content-Type: text/plain; charset="utf-8"; Format="flowed" On 9/9/20 8:48 AM, Hugh Parsonage wrote:> I am unable to set break or use gdb with any success when I use that version. > > On linux I would do R -d gdb but this gives "unknown option '-d' " > while gdb R.exe (in the same directory as the debug version) gives the > same output as before. > > I'm happy to help but I appreciate this list might not be the best > place to get a tutorial on using gdb on Windows.Essentially, the steps are: build with DEBUG=T (to have debug symbols), possibly updating EOPTS in MkRules.local to disable optimizations, then run gdb loading RGui, "set solib-search-path", run RGui from gdb. Then you can break to debugger from RGui menu, or just run the code that segfaults, and you get to gdb and can print the stacktrace, etc. You can find some information in rw-FAQ (R for Windows FAQ), but yes, it is harder than on Linux. We can take care of this report, but of course in the longer term it would help if more people could take their time to setup debugging and analyze bugs even on Windows. Tomas> > On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com> wrote: >> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote: >>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: >>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote: >>>>> Unfortunately I only get >>>>> >>>>> [Thread 21752.0x4aa8 exited with code 3221225477] >>>>> [Thread 21752.0x4514 exited with code 3221225477] >>>>> [Thread 21752.0x3f10 exited with code 3221225477] >>>>> [Inferior 1 (process 21752) exited with code 030000000005] >>>>> >>>>> (I'm guessing I would need to build an instrumented version of R, or >>>>> can R be debugged using gdb with an off-the-shelf installation?) >>>> No, the default build lacks debug symbols. You need a build with debug >>>> symbols, and if you can reproduce in a build without compiler >>>> optimizations (-O0), the backtrace may be easier to interpret. Some bugs >>>> however "disappear" when optimizations are disabled. You can build R >>>> from source (and there may be debug builds provided by someone else >>>> (Jeroen?)). >>> Debug builds for each revision are available from >>> https://r-devel.github.io . To download the installer you need to >>> click the github icon in the last column in the table. You need to be >>> signed in with a (free) Github account in order to download builds >>> (artifacts) from Github actions. It will show download links for both >>> the regular installer and installer with debug symbols. >>> >>> In other news, the https://r-devel.github.io table also shows that the >>> fix that martin committed is segfaulting on 32-bit. >> Sorry that was inaccurate, it is not segfaulting at all, but the unit >> test is raising an error on 32-bit.------------------------------ Message: 24 Date: Wed, 9 Sep 2020 17:30:17 +1000 From: Hugh Parsonage <hugh.parsonage at gmail.com> To: Tomas Kalibera <tomas.kalibera at gmail.com> Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney <luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>, Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re: [Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows Message-ID: <CAJmOi+MKW_RbxvVOfPDA58aYPzNz8ViKsVa+30ERsjmsV5Je+A at mail.gmail.com> Content-Type: text/plain; charset="utf-8" Thank you! I get Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe [New Thread 19940.0x638c] [New Thread 19940.0x102c] [New Thread 19940.0x329c] [New Thread 19940.0x37dc] warning: Invalid parameter passed to C runtime function. Program received signal SIGSEGV, Segmentation fault. 0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350, writeable=<optimized out>) at altclasses.c:169 169 altclasses.c: No such file or directory. On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at gmail.com> wrote:> > On 9/9/20 8:48 AM, Hugh Parsonage wrote: > > I am unable to set break or use gdb with any success when I use that version. > > > > On linux I would do R -d gdb but this gives "unknown option '-d' " > > while gdb R.exe (in the same directory as the debug version) gives the > > same output as before. > > > > I'm happy to help but I appreciate this list might not be the best > > place to get a tutorial on using gdb on Windows. > > Essentially, the steps are: build with DEBUG=T (to have debug symbols), > possibly updating EOPTS in MkRules.local to disable optimizations, then > run gdb loading RGui, "set solib-search-path", run RGui from gdb. Then > you can break to debugger from RGui menu, or just run the code that > segfaults, and you get to gdb and can print the stacktrace, etc. You can > find some information in rw-FAQ (R for Windows FAQ), but yes, it is > harder than on Linux. We can take care of this report, but of course in > the longer term it would help if more people could take their time to > setup debugging and analyze bugs even on Windows. > > Tomas > > > > > On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com> wrote: > >> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote: > >>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > >>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote: > >>>>> Unfortunately I only get > >>>>> > >>>>> [Thread 21752.0x4aa8 exited with code 3221225477] > >>>>> [Thread 21752.0x4514 exited with code 3221225477] > >>>>> [Thread 21752.0x3f10 exited with code 3221225477] > >>>>> [Inferior 1 (process 21752) exited with code 030000000005] > >>>>> > >>>>> (I'm guessing I would need to build an instrumented version of R, or > >>>>> can R be debugged using gdb with an off-the-shelf installation?) > >>>> No, the default build lacks debug symbols. You need a build with debug > >>>> symbols, and if you can reproduce in a build without compiler > >>>> optimizations (-O0), the backtrace may be easier to interpret. Some bugs > >>>> however "disappear" when optimizations are disabled. You can build R > >>>> from source (and there may be debug builds provided by someone else > >>>> (Jeroen?)). > >>> Debug builds for each revision are available from > >>> https://r-devel.github.io . To download the installer you need to > >>> click the github icon in the last column in the table. You need to be > >>> signed in with a (free) Github account in order to download builds > >>> (artifacts) from Github actions. It will show download links for both > >>> the regular installer and installer with debug symbols. > >>> > >>> In other news, the https://r-devel.github.io table also shows that the > >>> fix that martin committed is segfaulting on 32-bit. > >> Sorry that was inaccurate, it is not segfaulting at all, but the unit > >> test is raising an error on 32-bit. > >------------------------------ Message: 25 Date: Wed, 9 Sep 2020 08:00:41 +0000 From: "Koenker, Roger W" <rkoenker at illinois.edu> To: r-devel <r-devel at r-project.org> Subject: [Rd] Environmental Messaging Message-ID: <6C9F497D-5CEA-4A02-B7AB-490AB4022BB6 at illinois.edu> Content-Type: text/plain; charset="utf-8" What sort of message is this to send to the younger generation?> plastic = 1:5 > card = 1:4 > board = 1:4 > plastic/crossprod(card,board)[1] 0.03333333 0.06666667 0.10000000 0.13333333 0.16666667 Warning message: In plastic/crossprod(card, board) : Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead. ok, I can write c(crossprod()) but it is ugly, and environmentally wasteful. What?s next? Warnings for my beloved outer(card, board) * board ------------------------------ Message: 26 Date: Wed, 9 Sep 2020 10:00:55 +0200 From: Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh Parsonage <hugh.parsonage at gmail.com> Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney <luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>, Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re: [Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows Message-ID: <8383dabf-9093-41ea-2407-8bd75a1009e2 at gmail.com> Content-Type: text/plain; charset="utf-8"; Format="flowed" On 9/9/20 9:30 AM, Hugh Parsonage wrote:> Thank you! > > I get > > Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe > [New Thread 19940.0x638c] > [New Thread 19940.0x102c] > [New Thread 19940.0x329c] > [New Thread 19940.0x37dc] > warning: Invalid parameter passed to C runtime function. > > Program received signal SIGSEGV, Segmentation fault. > 0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350, > writeable=<optimized out>) at altclasses.c:169 > 169 altclasses.c: No such file or directory.Thanks, would you know which svn version this is? Tomas> > On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at gmail.com> wrote: >> On 9/9/20 8:48 AM, Hugh Parsonage wrote: >>> I am unable to set break or use gdb with any success when I use that version. >>> >>> On linux I would do R -d gdb but this gives "unknown option '-d' " >>> while gdb R.exe (in the same directory as the debug version) gives the >>> same output as before. >>> >>> I'm happy to help but I appreciate this list might not be the best >>> place to get a tutorial on using gdb on Windows. >> Essentially, the steps are: build with DEBUG=T (to have debug symbols), >> possibly updating EOPTS in MkRules.local to disable optimizations, then >> run gdb loading RGui, "set solib-search-path", run RGui from gdb. Then >> you can break to debugger from RGui menu, or just run the code that >> segfaults, and you get to gdb and can print the stacktrace, etc. You can >> find some information in rw-FAQ (R for Windows FAQ), but yes, it is >> harder than on Linux. We can take care of this report, but of course in >> the longer term it would help if more people could take their time to >> setup debugging and analyze bugs even on Windows. >> >> Tomas >> >>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com> wrote: >>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote: >>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: >>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote: >>>>>>> Unfortunately I only get >>>>>>> >>>>>>> [Thread 21752.0x4aa8 exited with code 3221225477] >>>>>>> [Thread 21752.0x4514 exited with code 3221225477] >>>>>>> [Thread 21752.0x3f10 exited with code 3221225477] >>>>>>> [Inferior 1 (process 21752) exited with code 030000000005] >>>>>>> >>>>>>> (I'm guessing I would need to build an instrumented version of R, or >>>>>>> can R be debugged using gdb with an off-the-shelf installation?) >>>>>> No, the default build lacks debug symbols. You need a build with debug >>>>>> symbols, and if you can reproduce in a build without compiler >>>>>> optimizations (-O0), the backtrace may be easier to interpret. Some bugs >>>>>> however "disappear" when optimizations are disabled. You can build R >>>>>> from source (and there may be debug builds provided by someone else >>>>>> (Jeroen?)). >>>>> Debug builds for each revision are available from >>>>> https://r-devel.github.io . To download the installer you need to >>>>> click the github icon in the last column in the table. You need to be >>>>> signed in with a (free) Github account in order to download builds >>>>> (artifacts) from Github actions. It will show download links for both >>>>> the regular installer and installer with debug symbols. >>>>> >>>>> In other news, the https://r-devel.github.io table also shows that the >>>>> fix that martin committed is segfaulting on 32-bit. >>>> Sorry that was inaccurate, it is not segfaulting at all, but the unit >>>> test is raising an error on 32-bit. >>------------------------------ Message: 27 Date: Wed, 9 Sep 2020 18:32:58 +1000 From: Hugh Parsonage <hugh.parsonage at gmail.com> To: Tomas Kalibera <tomas.kalibera at gmail.com> Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney <luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>, Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re: [Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows Message-ID: <CAJmOi+MLyn_WcBLFSQdL9ze4iDzazysPcU7QGOQtWryTod44Yg at mail.gmail.com> Content-Type: text/plain; charset="utf-8" R Under development (unstable) (2020-09-08 r79165) On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera <tomas.kalibera at gmail.com> wrote:> > On 9/9/20 9:30 AM, Hugh Parsonage wrote: > > Thank you! > > > > I get > > > > Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe > > [New Thread 19940.0x638c] > > [New Thread 19940.0x102c] > > [New Thread 19940.0x329c] > > [New Thread 19940.0x37dc] > > warning: Invalid parameter passed to C runtime function. > > > > Program received signal SIGSEGV, Segmentation fault. > > 0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350, > > writeable=<optimized out>) at altclasses.c:169 > > 169 altclasses.c: No such file or directory. > > Thanks, would you know which svn version this is? > > Tomas > > > > > On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > >> On 9/9/20 8:48 AM, Hugh Parsonage wrote: > >>> I am unable to set break or use gdb with any success when I use that version. > >>> > >>> On linux I would do R -d gdb but this gives "unknown option '-d' " > >>> while gdb R.exe (in the same directory as the debug version) gives the > >>> same output as before. > >>> > >>> I'm happy to help but I appreciate this list might not be the best > >>> place to get a tutorial on using gdb on Windows. > >> Essentially, the steps are: build with DEBUG=T (to have debug symbols), > >> possibly updating EOPTS in MkRules.local to disable optimizations, then > >> run gdb loading RGui, "set solib-search-path", run RGui from gdb. Then > >> you can break to debugger from RGui menu, or just run the code that > >> segfaults, and you get to gdb and can print the stacktrace, etc. You can > >> find some information in rw-FAQ (R for Windows FAQ), but yes, it is > >> harder than on Linux. We can take care of this report, but of course in > >> the longer term it would help if more people could take their time to > >> setup debugging and analyze bugs even on Windows. > >> > >> Tomas > >> > >>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com> wrote: > >>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote: > >>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > >>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote: > >>>>>>> Unfortunately I only get > >>>>>>> > >>>>>>> [Thread 21752.0x4aa8 exited with code 3221225477] > >>>>>>> [Thread 21752.0x4514 exited with code 3221225477] > >>>>>>> [Thread 21752.0x3f10 exited with code 3221225477] > >>>>>>> [Inferior 1 (process 21752) exited with code 030000000005] > >>>>>>> > >>>>>>> (I'm guessing I would need to build an instrumented version of R, or > >>>>>>> can R be debugged using gdb with an off-the-shelf installation?) > >>>>>> No, the default build lacks debug symbols. You need a build with debug > >>>>>> symbols, and if you can reproduce in a build without compiler > >>>>>> optimizations (-O0), the backtrace may be easier to interpret. Some bugs > >>>>>> however "disappear" when optimizations are disabled. You can build R > >>>>>> from source (and there may be debug builds provided by someone else > >>>>>> (Jeroen?)). > >>>>> Debug builds for each revision are available from > >>>>> https://r-devel.github.io . To download the installer you need to > >>>>> click the github icon in the last column in the table. You need to be > >>>>> signed in with a (free) Github account in order to download builds > >>>>> (artifacts) from Github actions. It will show download links for both > >>>>> the regular installer and installer with debug symbols. > >>>>> > >>>>> In other news, the https://r-devel.github.io table also shows that the > >>>>> fix that martin committed is segfaulting on 32-bit. > >>>> Sorry that was inaccurate, it is not segfaulting at all, but the unit > >>>> test is raising an error on 32-bit. > >> >------------------------------ Message: 28 Date: Wed, 9 Sep 2020 10:53:18 +0200 From: Tomas Kalibera <tomas.kalibera at gmail.com> To: Hugh Parsonage <hugh.parsonage at gmail.com> Cc: Jeroen Ooms <jeroenooms at gmail.com>, Luke Tierney <luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>, Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re: [Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows Message-ID: <6b01fb27-ec83-4dea-6478-c344f285083b at gmail.com> Content-Type: text/plain; charset="utf-8"; Format="flowed" Thanks. Should be now fixed in 79169. Tomas On 9/9/20 10:32 AM, Hugh Parsonage wrote:> R Under development (unstable) (2020-09-08 r79165) > > On Wed, 9 Sep 2020 at 18:00, Tomas Kalibera <tomas.kalibera at gmail.com> wrote: >> On 9/9/20 9:30 AM, Hugh Parsonage wrote: >>> Thank you! >>> >>> I get >>> >>> Starting program: C:\R\R-devel-20200909\bin\x64\Rgui.exe >>> [New Thread 19940.0x638c] >>> [New Thread 19940.0x102c] >>> [New Thread 19940.0x329c] >>> [New Thread 19940.0x37dc] >>> warning: Invalid parameter passed to C runtime function. >>> >>> Program received signal SIGSEGV, Segmentation fault. >>> 0x000000006c72d206 in compact_intseq_Dataptr (x=0x12783350, >>> writeable=<optimized out>) at altclasses.c:169 >>> 169 altclasses.c: No such file or directory. >> Thanks, would you know which svn version this is? >> >> Tomas >> >>> On Wed, 9 Sep 2020 at 17:03, Tomas Kalibera <tomas.kalibera at gmail.com> wrote: >>>> On 9/9/20 8:48 AM, Hugh Parsonage wrote: >>>>> I am unable to set break or use gdb with any success when I use that version. >>>>> >>>>> On linux I would do R -d gdb but this gives "unknown option '-d' " >>>>> while gdb R.exe (in the same directory as the debug version) gives the >>>>> same output as before. >>>>> >>>>> I'm happy to help but I appreciate this list might not be the best >>>>> place to get a tutorial on using gdb on Windows. >>>> Essentially, the steps are: build with DEBUG=T (to have debug symbols), >>>> possibly updating EOPTS in MkRules.local to disable optimizations, then >>>> run gdb loading RGui, "set solib-search-path", run RGui from gdb. Then >>>> you can break to debugger from RGui menu, or just run the code that >>>> segfaults, and you get to gdb and can print the stacktrace, etc. You can >>>> find some information in rw-FAQ (R for Windows FAQ), but yes, it is >>>> harder than on Linux. We can take care of this report, but of course in >>>> the longer term it would help if more people could take their time to >>>> setup debugging and analyze bugs even on Windows. >>>> >>>> Tomas >>>> >>>>> On Wed, 9 Sep 2020 at 07:47, Jeroen Ooms <jeroenooms at gmail.com> wrote: >>>>>> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote: >>>>>>> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: >>>>>>>> On 9/8/20 4:48 PM, Hugh Parsonage wrote: >>>>>>>>> Unfortunately I only get >>>>>>>>> >>>>>>>>> [Thread 21752.0x4aa8 exited with code 3221225477] >>>>>>>>> [Thread 21752.0x4514 exited with code 3221225477] >>>>>>>>> [Thread 21752.0x3f10 exited with code 3221225477] >>>>>>>>> [Inferior 1 (process 21752) exited with code 030000000005] >>>>>>>>> >>>>>>>>> (I'm guessing I would need to build an instrumented version of R, or >>>>>>>>> can R be debugged using gdb with an off-the-shelf installation?) >>>>>>>> No, the default build lacks debug symbols. You need a build with debug >>>>>>>> symbols, and if you can reproduce in a build without compiler >>>>>>>> optimizations (-O0), the backtrace may be easier to interpret. Some bugs >>>>>>>> however "disappear" when optimizations are disabled. You can build R >>>>>>>> from source (and there may be debug builds provided by someone else >>>>>>>> (Jeroen?)). >>>>>>> Debug builds for each revision are available from >>>>>>> https://r-devel.github.io . To download the installer you need to >>>>>>> click the github icon in the last column in the table. You need to be >>>>>>> signed in with a (free) Github account in order to download builds >>>>>>> (artifacts) from Github actions. It will show download links for both >>>>>>> the regular installer and installer with debug symbols. >>>>>>> >>>>>>> In other news, the https://r-devel.github.io table also shows that the >>>>>>> fix that martin committed is segfaulting on 32-bit. >>>>>> Sorry that was inaccurate, it is not segfaulting at all, but the unit >>>>>> test is raising an error on 32-bit.------------------------------ Message: 29 Date: Wed, 9 Sep 2020 11:06:12 +0200 From: Tomas Kalibera <tomas.kalibera at gmail.com> To: Jeroen Ooms <jeroenooms at gmail.com> Cc: Hugh Parsonage <hugh.parsonage at gmail.com>, Luke Tierney <luke-tierney at uiowa.edu>, R-devel <r-devel at r-project.org>, Martin Maechler <maechler at stat.math.ethz.ch> Subject: Re: [Rd] [External] Re: Operations with long altrep vectors cause segfaults on Windows Message-ID: <5fd517e2-ad46-c343-2a63-cda01ff58acc at gmail.com> Content-Type: text/plain; charset="utf-8"; Format="flowed" On 9/8/20 11:47 PM, Jeroen Ooms wrote:> On Tue, Sep 8, 2020 at 11:44 PM Jeroen Ooms <jeroenooms at gmail.com> wrote: >> On Tue, Sep 8, 2020 at 5:20 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: >>> On 9/8/20 4:48 PM, Hugh Parsonage wrote: >>>> Unfortunately I only get >>>> >>>> [Thread 21752.0x4aa8 exited with code 3221225477] >>>> [Thread 21752.0x4514 exited with code 3221225477] >>>> [Thread 21752.0x3f10 exited with code 3221225477] >>>> [Inferior 1 (process 21752) exited with code 030000000005] >>>> >>>> (I'm guessing I would need to build an instrumented version of R, or >>>> can R be debugged using gdb with an off-the-shelf installation?) >>> No, the default build lacks debug symbols. You need a build with debug >>> symbols, and if you can reproduce in a build without compiler >>> optimizations (-O0), the backtrace may be easier to interpret. Some bugs >>> however "disappear" when optimizations are disabled. You can build R >>> from source (and there may be debug builds provided by someone else >>> (Jeroen?)). >> Debug builds for each revision are available from >> https://r-devel.github.io . To download the installer you need to >> click the github icon in the last column in the table. You need to be >> signed in with a (free) Github account in order to download builds >> (artifacts) from Github actions. It will show download links for both >> the regular installer and installer with debug symbols. >> >> In other news, the https://r-devel.github.io table also shows that the >> fix that martin committed is segfaulting on 32-bit. > Sorry that was inaccurate, it is not segfaulting at all, but the unit > test is raising an error on 32-bit.Now fixed, the test needs to be run only on 64-bit builds where such long vectors/sequences are allowed. Tomas ------------------------------ Subject: Digest Footer _______________________________________________ R-devel at r-project.org mailing list DIGESTED https://stat.ethz.ch/mailman/listinfo/r-devel ------------------------------ End of R-devel Digest, Vol 211, Issue 7 ***************************************
>>>>> 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
> > "These operators are also implicit S4 generics, but as > > primitives, S4 methods will be dispatched only on S4 > > objects ?x?."> Yes, exactly, very well found, Georgi!I'm sorry Martin, but I don't understand your point here. I'm assuming that you want the (S3) matrix, x, to be converted to an (S4) Matrix. However, this is not a question of method dispatch, as such. But rather a question of type conversion (integer to numeric to complex, etc). Specifically, can/should automatic type conversion, convert an S3 data type to an S4 data type, even where user-defined data types are involved?
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
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