Re: [R-pkg-devel] Valgrind warning on saveRDS, about object in external pointer
Thanks a lot for the answer!
I unfortunately wasn’t able to reproduce it with the same OS + compiler
+ valgrind settings, but from what I see in the message, turns out in
the end it might indeed be due to Cereal copying raw bytes into an R
vector and Valgrind complaining about the copied bytes rather than the
original object.
And it also looks like it could be issue with default initializations.
With this I’ve now learned that ‘Struct() {}’ and ‘Struct()=default’
are not the same thing.
Still, oddly enough that the complaint happens only at ‘saveRDS’ when
tested on the CRAN servers.
Thanks again for your help!
Best regards,
David Cortes
On Wed, 2020-07-15 at 16:51 +0300, Ivan Krylov wrote:
> On Wed, 08 Jul 2020 22:43:13 +0300
> David Cortes wrote:
>
> > About the source code: it actually complains about line
> > fit_model.cpp:751 :
> > hplane_root->reserve(exp_nodes);
>
> My fault. I was reading the GitHub source code instead of CRAN
> package
> source code.
>
> > I’m not able to reproduce the warning when trying R CMD check with
> > valgrind on my computer (tried compiling with gcc9 and clang9), nor
> > with the r-debug docker images from github (
> > https://github.com/wch/r-debug).
>
> My current system is amd64 Debian 9.12 (gcc 6.3.0-18+deb9u1) with R
> 3.6.3-1~stretchcran.0. I have built a package from the current GitHub
> source of the package and ran R -d 'valgrind --track-origins=yes'
> --vanilla < isotree-Ex.R. This resulted in multiple Valgrind warnings
> about accessing uninitialised values created by heap allocations at
> fit_model.cpp:783 and fit_model.cpp:788.
>
> The first such error can be traced to a pointer to
> ext_model_ptr->hplanes[0][2].remainder:
>
> (gdb) frame 2
> #2 cereal::BinaryOutputArchive::saveBinary (this=,
> data=data@entry=0x14a3ad40, size=size@entry=8)
> at /home/me/R/x86_64-pc-linux-gnu-
> library/3.6/Rcereal/include/cereal/archives/binary.hpp:67
> 67 auto const writtenSize = static_cast(
> itsStream.rdbuf()->sputn( reinterpret_cast( data ), size
> ) );
> (gdb) p data
> $19 = (const void *) 0x14a3ad40
> (gdb) frame 41
> #41 0x19d8ce38 in fit_model (X_num=..., X_cat=..., ncat=...,
> Xc=..., Xc_ind=..., Xc_indptr=..., sample_weights=...,
> col_weights=..., nrows=100,
> ncols_numeric=2, ncols_categ=0, ndim=2, ntry=3, coef_type=...,
> coef_by_prop=false, with_replacement=false, weight_as_sample=true,
> sample_size=100, ntrees=3,
> max_depth=7, limit_depth=false, penalize_range=true,
> calc_dist=false, standardize_dist=true, sq_dist=false,
> calc_depth=false, standardize_depth=true,
> weigh_by_kurt=false,
> prob_pick_by_gain_avg=prob_pick_by_gain_avg@entry=0,
> prob_split_by_gain_avg=prob_split_by_gain_avg@entry=0,
> prob_pick_by_gain_pl=prob_pick_by_gain_pl@entry=0,
> prob_split_by_gain_pl=prob_split_by_gain_pl@entry=0,
> min_gain=min_gain@entry=0, cat_split_type=...,
> new_cat_action=..., missing_action=..., all_perm=false,
> build_imputer=false, output_imputations=false, min_imp_obs=3,
> depth_imp=..., weigh_imp_rows=...,
> random_seed=1, nthreads=1) at Rwrapper.cpp:320
> 320 serialized_obj = serialize_cpp_obj(ext_model_ptr.get())
> ;
> (gdb) p _model_ptr->hplanes[0][2].remainder
> $20 = (double *) 0x14a3ad40
>
> (In some stack frames gdb helpfully says that the pointer is
> optimised
> out, but in others it can be accessed.)
>
> I grepped the source code for 'remainder =' and found one assignment
> to
> hplanes.back().remainder in extended.cpp:507. Could
> hplanes.emplace_back() happen without a corresponding assignment to
> hplanes.back().remainder?
>
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Re: [R-pkg-devel] Anyone Know How To Setup Wine for Windows Testing?
If you don't mind multi-gig docker containers, this can be helpful: https://github.com/scottyhardy/docker-wine It doesn't work with 64 bit versions of R as far as I could tell, but 32 bit did install and start correctly in a few clicks when I tried last year. On Wed, Jul 15, 2020 at 10:56 AM J C Nash wrote: > Are you sure you want to try to run R etc. under Wine? > > - If you have Windows running, either directly or in a VM, you can run R > there. > - If you have Windows and want to run R under some other OS, then set up a > VM > e.g., Linux Mint, for that. I sometimes test R for Windows in a VirtualBox > VM > for Win10, but generally run in Linux Mint. I've also run R in some Linux > VMs > to test for specific dependencies in some distros. > > I rather doubt R will run very well in Linux under Wine. My experience > with Wine > is that a few apps (e.g. Irfanview) run well, but many give lots of > trouble. > > JN > > > On 2020-07-15 1:17 p.m., Steve Bronder wrote: > > Does anyone know of a setup guide for getting R and Rtools 4.0 up and > > running on Wine with the Windows Server 2008 R2 VM? Do other maintainers > > with more knowhow think that would be useful for debugging purposes? > > > > I've been trying to test out some flto gcc things for windows by setting > up > > a local wine VM on my ubuntu box. Wine has an option for Windows Server > > 2008 R2 (which I believe is the windows session CRAN uses?) If anyone has > > done this before and knows of a guide somewhere that would be very > helpful! > > > > Regards, > > > > Steve Bronder > > > > [[alternative HTML version deleted]] > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Anyone Know How To Setup Wine for Windows Testing?
Are you sure you want to try to run R etc. under Wine? - If you have Windows running, either directly or in a VM, you can run R there. - If you have Windows and want to run R under some other OS, then set up a VM e.g., Linux Mint, for that. I sometimes test R for Windows in a VirtualBox VM for Win10, but generally run in Linux Mint. I've also run R in some Linux VMs to test for specific dependencies in some distros. I rather doubt R will run very well in Linux under Wine. My experience with Wine is that a few apps (e.g. Irfanview) run well, but many give lots of trouble. JN On 2020-07-15 1:17 p.m., Steve Bronder wrote: > Does anyone know of a setup guide for getting R and Rtools 4.0 up and > running on Wine with the Windows Server 2008 R2 VM? Do other maintainers > with more knowhow think that would be useful for debugging purposes? > > I've been trying to test out some flto gcc things for windows by setting up > a local wine VM on my ubuntu box. Wine has an option for Windows Server > 2008 R2 (which I believe is the windows session CRAN uses?) If anyone has > done this before and knows of a guide somewhere that would be very helpful! > > Regards, > > Steve Bronder > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Anyone Know How To Setup Wine for Windows Testing?
Does anyone know of a setup guide for getting R and Rtools 4.0 up and running on Wine with the Windows Server 2008 R2 VM? Do other maintainers with more knowhow think that would be useful for debugging purposes? I've been trying to test out some flto gcc things for windows by setting up a local wine VM on my ubuntu box. Wine has an option for Windows Server 2008 R2 (which I believe is the windows session CRAN uses?) If anyone has done this before and knows of a guide somewhere that would be very helpful! Regards, Steve Bronder [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Valgrind warning on saveRDS, about object in external pointer
On Wed, 08 Jul 2020 22:43:13 +0300 David Cortes wrote: > About the source code: it actually complains about line > fit_model.cpp:751 : > hplane_root->reserve(exp_nodes); My fault. I was reading the GitHub source code instead of CRAN package source code. > I’m not able to reproduce the warning when trying R CMD check with > valgrind on my computer (tried compiling with gcc9 and clang9), nor > with the r-debug docker images from github ( > https://github.com/wch/r-debug). My current system is amd64 Debian 9.12 (gcc 6.3.0-18+deb9u1) with R 3.6.3-1~stretchcran.0. I have built a package from the current GitHub source of the package and ran R -d 'valgrind --track-origins=yes' --vanilla < isotree-Ex.R. This resulted in multiple Valgrind warnings about accessing uninitialised values created by heap allocations at fit_model.cpp:783 and fit_model.cpp:788. The first such error can be traced to a pointer to ext_model_ptr->hplanes[0][2].remainder: (gdb) frame 2 #2 cereal::BinaryOutputArchive::saveBinary (this=, data=data@entry=0x14a3ad40, size=size@entry=8) at /home/me/R/x86_64-pc-linux-gnu-library/3.6/Rcereal/include/cereal/archives/binary.hpp:67 67 auto const writtenSize = static_cast( itsStream.rdbuf()->sputn( reinterpret_cast( data ), size ) ); (gdb) p data $19 = (const void *) 0x14a3ad40 (gdb) frame 41 #41 0x19d8ce38 in fit_model (X_num=..., X_cat=..., ncat=..., Xc=..., Xc_ind=..., Xc_indptr=..., sample_weights=..., col_weights=..., nrows=100, ncols_numeric=2, ncols_categ=0, ndim=2, ntry=3, coef_type=..., coef_by_prop=false, with_replacement=false, weight_as_sample=true, sample_size=100, ntrees=3, max_depth=7, limit_depth=false, penalize_range=true, calc_dist=false, standardize_dist=true, sq_dist=false, calc_depth=false, standardize_depth=true, weigh_by_kurt=false, prob_pick_by_gain_avg=prob_pick_by_gain_avg@entry=0, prob_split_by_gain_avg=prob_split_by_gain_avg@entry=0, prob_pick_by_gain_pl=prob_pick_by_gain_pl@entry=0, prob_split_by_gain_pl=prob_split_by_gain_pl@entry=0, min_gain=min_gain@entry=0, cat_split_type=..., new_cat_action=..., missing_action=..., all_perm=false, build_imputer=false, output_imputations=false, min_imp_obs=3, depth_imp=..., weigh_imp_rows=..., random_seed=1, nthreads=1) at Rwrapper.cpp:320 320 serialized_obj = serialize_cpp_obj(ext_model_ptr.get()); (gdb) p _model_ptr->hplanes[0][2].remainder $20 = (double *) 0x14a3ad40 (In some stack frames gdb helpfully says that the pointer is optimised out, but in others it can be accessed.) I grepped the source code for 'remainder =' and found one assignment to hplanes.back().remainder in extended.cpp:507. Could hplanes.emplace_back() happen without a corresponding assignment to hplanes.back().remainder? -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
