[Rcpp-devel] Any recent change that would remove Rcpp_precious_remove?

Dominick Samperi djsamperi at gmail.com
Sat Oct 2 04:10:14 CEST 2021


I forgot to mention, this testing was done using R 4.1.1, Rcpp 1.0.7, and
RInside 0.2.16, using MacOS version 10.15.7 (Catalina), and Apple clang
version 12.0.0.

On Fri, Oct 1, 2021 at 9:50 PM Dominick Samperi <djsamperi at gmail.com> wrote:

> Hello Dirk,
>
> I have what appears to be a reproducible example of the
> "Rcpp_precious_remove"
> problem that a few people have complained about. It is reproducible on my
> Mac Mini, but may not appears when you try because it is OS and compiler
> dependent. There is no problem under Windows, for example. There
> seems to be a gc bug lurking.
>
> The test C++ source file (a simple REPL loop), makefile, and
> lldb (debugger) backtrace are attached to this message.
> When I compile and run on my Mac is fails with a seg fault every time.
>
> I have been able to trigger this problem
> under Ubuntu in a more complicated project using CMake. It
> fails every time. Furthermore, gdb shows that the failure happens on
> line 261 of RInside.cpp (where global_env_m = new Rcpp::Environment()).
>
> The comment immediately above this failure point says
> there is exposure to "a minimal risk of garbage collection" (based on
> feedback from Doug Bates and Luke Tierney). Perhaps the risk is greater
> than you anticipated?
>
> BTW, if I build the REPL app and link to a locally built version of
> RInside library, and not to the version installed by R, the REPL
> app works on my Mac Mini! This is probably due to the fact
> that stack/heap corruption can reveal itself in mysterious ways
> depending on the precise configuration employed.
>
> Thanks,
> Dominick
>
>
> On Thu, Jul 15, 2021 at 8:13 AM Dirk Eddelbuettel <edd at debian.org> wrote:
>
>>
>> On 15 July 2021 at 08:24, ma wh wrote:
>> | Colleague of mine wrote some R last week that was working OK, and
>> hasn't been changed in itself since that time. This week it's ceased
>> working( I've tried it on my machine and also see a fail, the following
>> error is encountered:
>> |
>> | Error in C_valid_tz(tzone): Function 'Rcpp_precious_remove' not
>> provided by package 'Rcpp'
>> |
>> | Searching around there aren't many hits. Those I do find seem quite
>> recent (stackoverflow questions or GitHub issues logged in various
>> projects, dates of posting are within the last few days). None of the
>> posted queries seem to have a solution, one person said restarting RStudio
>> helped, but not in my case. The SO question I found was marked as deleted.
>> The GitHub issue I found was "I solved it" but no mention of how. The SO
>> question was asking about svg export:
>> https://stackoverflow.com/questions/68345118/exporting-a-ggplot-in-svg-call-a-non-esixting-function
>> | The GitHub were also asking about packages I don't use -
>> | https://github.com/r-spatial/spdep/issues/60
>> | https://github.com/drizopoulos/JMbayes2/issues/5
>> |
>> | Anyone on the list have any pointers? Thanks
>>
>> Packages following a the GNU style often have a file ChangeLog which
>> "details
>> changes made to the code". Rcpp follows this convention, see 2021-07-05
>> and
>> 2021-01-017.
>>
>> Packages following the R packaging conventions often have a file
>> inst/NEWS.rd
>> (also rendered as NEWS at CRAN). Rcpp follow this conventions, see the
>> Rcpp
>> 1.0.7 release (even if the functions is not named).
>>
>> Packages have source code you can search.I like `ag` aka "the
>> silversearcher":
>>
>>   edd at rob:~/git/rcpp(master)$ ag -c Rcpp_precious_remove
>>   ChangeLog:2
>>   inst/include/Rcpp/routines.h:3
>>   inst/include/RcppCommon.h:2
>>   src/rcpp_init.cpp:1
>>   src/barrier.cpp:1
>>   edd at rob:~/git/rcpp(master)$
>>
>> It is still there, and available via the standard export mechanism.
>>
>> I recommend your friend take a look. The function is a) still there yet
>> has
>> also b) been supplanted by a more sufficient alternative.
>>
>> Otherwise, a reproducible example would be the only way to make this
>> concrete.
>>
>> Hope this helps, Dirk
>>
>> --
>> https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>> _______________________________________________
>> Rcpp-devel mailing list
>> Rcpp-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>
>
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