[R-pkg-devel] Solaris segfaults

[Ben Bolker]

  I think I got confused by the fact that the second line of

https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-patched-solaris-x86
is "Solaris 10 on ix64/x64".

   I interpreted that as "64-bit Solaris".  On the other hand the rest 
of the information in that file says that the default ODS compiler used 
is a 32-bit build; it doesn't say anything about the build of the 
alternative gcc compiler (which is used for packages with Rcpp etc.) 
Other comments farther down in the file (about versions of Java, 
protobuf used) do suggest that the system is indeed 32-bit.

  If the CRAN Solaris platform is indeed 32-bit, then I really have no 
idea why checks are failing on CRAN but succeeding on r-hub (but I also 
feel better about not trying to fix it ...)

   I do appreciate the provision of the resources for setting up a 
virtual Solaris box - I don't recall exactly what hurdle I encountered 
last time I tried, it was probably some weird idiosyncratic thing.

   For the record I haven't tried valgrind recently, but the CRAN 
versions of the valgrind tests weren't throwing any errors ... 
https://cran.r-project.org/web/checks/check_issue_kinds.html

   thanks
    Ben Bolker


On 9/15/21 2:19 AM, Gábor Csárdi wrote:
> Hi Ben,
> 
> According to https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-patched-solaris-x86
> CRAN's Solaris is also 32 bit.
> But maybe I am missing something?
> 
> You can download a Solaris VM (for Virtualbox or VMware) from
> https://files.r-hub.io/solaris/
> It has both 32 bit and 64 bit R (with gcc) and ODS R as well. You can
> update R on it like this:
> https://github.com/r-hub/solarischeck/tree/master/packer#updating-r
> 
> Best,
> Gabor
> 
> On Wed, Sep 15, 2021 at 1:51 AM Ben Bolker <bbolker using gmail.com> wrote:
>>
>>     I may have asked something like this before, but ...
>>
>> The glmmTMB package is currently segfaulting (on the very first example)
>> on its CRAN Solaris checks
>> https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/glmmTMB-00check.html
>>
>> ----
>>   > ## Comparing variance-covariance matrix with manual computation
>>   > data("sleepstudy",package="lme4")
>>   > fm4 <- glmmTMB(Reaction ~ Days + (Days|Subject), sleepstudy)
>>
>>    *** caught segfault ***
>> address 4539ec45, cause 'memory not mapped'
>> ---
>>
>>
>>
>>    We have to submit a new version to CRAN soon; we will most likely beg
>> the CRAN maintainers' indulgence for having it fail on Solaris, but it
>> would be nice to fix it if we can.
>>
>>      The CRAN Solaris platform is 64-bit x86_64, using gcc/g++ because
>> the package uses Rcpp.
>>
>>     The package builds/checks fine on the r-hub `solaris-x86-patched`
>> platform, which is identical as far as I can tell **except** 32-bit
>> rather than 64-bit.
>>
>>     Short of installing 64-bit Solaris in a VM (which I have not done yet
>> because of random compatibility/command-line bullshittery that put me
>> off), does anyone have any wisdom to share for diagnosing and/or
>> guessing what the problem is?
>>
>>     Here are some links to similar errors, none of them seem terribly
>> useful/relevant.
>>
>> https://github.com/gagolews/stringi/issues/94
>> https://mran.microsoft.com/snapshot/2017-07-05/web/checks/check_results_vcfR.html
>> https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/prt-00check.html
>>
>>     glmmTMB is built on a pretty big stack (Eigen, Rcpp, RcppEigen,
>> CppAD, TMB) - the problem could be somewhere in there (the TMB package
>> runs no tests and very few examples on CRAN, so there could be problems
>> there that only get flagged when we try glmmTMB examples).
>>
>> More discussion at
>>    https://github.com/glmmTMB/glmmTMB/issues/732 (with some red herrings)
>> if anyone is interested.
>>
>>     cheers
>>      Ben Bolker
>>
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>> R-package-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel

-- 
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
Graduate chair, Mathematics & Statistics