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<p>I was finally able to get reproducible, although likely not minimal segfault even without Rstudio. I built a new package and running a weird loop with rebuilding of the source files and doing some other random stuff as well, I was able to get a segfault.
valgrind output looks like this:</p>
<pre><code><span style="font-size: 8pt;">==26398== Jump to the invalid address stated on the next line
==26398== at 0x1DD75010: ???
==26398== by 0x4F7D026: R_RunWeakRefFinalizer (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F7D213: ??? (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F4A679: Rf_eval (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F4EA11: ??? (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F4AB99: Rf_eval (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F4D723: ??? (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F4AA9F: Rf_eval (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F4CABE: ??? (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F42F67: ??? (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F50D55: ??? (in /usr/lib/R/lib/libR.so)
==26398== by 0x4F512FF: ??? (in /usr/lib/R/lib/libR.so)
==26398== Address 0x1dd75010 is not stack'd, malloc'd or (recently) free'd
==26398==
*** caught segfault ***
address 0x1dd75010, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
==26398==
==26398== Process terminating with default action of signal 11 (SIGSEGV)
==26398== at 0x547451D: raise (raise.c:53)
==26398== by 0x547466F: ??? (in /lib/x86_64-linux-gnu/libpthread-2.24.so)
==26398== by 0x1DD7500F: ???
==26398==
==26398== HEAP SUMMARY:
==26398== in use at exit: 259,162,338 bytes in 28,465 blocks
==26398== total heap usage: 315,728 allocs, 287,263 frees, 1,311,929,706 bytes allocated
==26398==
==26398== LEAK SUMMARY:
==26398== definitely lost: 0 bytes in 0 blocks
==26398== indirectly lost: 0 bytes in 0 blocks
==26398== possibly lost: 0 bytes in 0 blocks
==26398== still reachable: 259,162,338 bytes in 28,465 blocks
==26398== of which reachable via heuristic:
==26398== newarray : 4,264 bytes in 1 blocks
==26398== suppressed: 0 bytes in 0 blocks
==26398== Reachable blocks (those to which a pointer was found) are not shown.
==26398== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==26398==
==26398== For counts of detected and suppressed errors, rerun with: -v
==26398== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)</span>
</code></pre>
<p>What is super weird is that currently I have this extra C++ function which is not even used at all:</p>
<pre><code><span style="font-size: 8pt;">double log_prior_pdf(const arma::vec& theta) {
double log_pdf = 0.0;
double infinite = -arma::datum::inf; //comment out this line and everything works??
return log_pdf;
}</span></code></pre>
If I remove the middle line, I seem to get rid of the segfault. <span>However, I also have some extra stuff on the R script (crash.R) as well which looks to be necessary for the segfault to trigger at certain point (third iteration of the outer loop).</span></div>
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<p>Jouni<br>
</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>Lähettäjä:</b> Dirk Eddelbuettel <dirk.eddelbuettel@gmail.com> käyttäjän Dirk Eddelbuettel <edd@debian.org> puolesta<br>
<b>Lähetetty:</b> maanantai 4. syyskuuta 2017 15.32.13<br>
<b>Vastaanottaja:</b> Helske, Jouni<br>
<b>Kopio:</b> Rcpp-devel@lists.r-forge.r-project.org<br>
<b>Aihe:</b> Re: [Rcpp-devel] Rstudio crashes with repeated calls to sourceCpp with Xptr export</font>
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Hi Jouni,<br>
<br>
On 4 September 2017 at 08:22, Helske, Jouni wrote:<br>
| In the bssm package (<a href="https://github.com/helske/bssm" id="LPlnk400281" previewremoved="true">https://github.com/helske/bssm</a>), I let the users<br>
| define a state space model via own C++ functions which are then exported as<br>
| Xptr to R side, and passed back to C++ function for SMC/MCMC etc. Normally<br>
| this works fine, but when user repeatedly modifies the model functions and<br>
| re-exports them via repeated calls sourceCpp, sometimes whole Rstudio<br>
| crashes.<br>
<br>
Which version of RStudio? See Help -> About<br>
<br>
| I haven't been able to pinpoint the reason or minimal example. Have anyone else experienced similar issues or is it just me i.e. error in my own implementations?<br>
<br>
There are a lot of dependencies here [re-indented by me]:<br>
<br>
Suggests: KFAS (>= 1.2.1), knitr (>= 1.11), rmarkdown (>= 0.8.1), testthat,<br>
bayesplot<br>
Imports: coda (>= 0.18-1), diagis, ggplot2 (>= 2.0.0), Rcpp (>= 0.12.3)<br>
LinkingTo: BH, Rcpp, RcppArmadillo, ramcmc, sitmo<br>
<br>
We do know Boost interactions (between code compiled 'by us' as R extensions<br>
using Boost, and RStudio itself also using an older version of Boost) had<br>
thrown spanners in the past. A while back Kevin updated RStudio internals and<br>
shielded "their" Boost better.<br>
<br>
I happen to run RStudio "Daily" builds on all my machines -- those have the<br>
fix and "behave". Maybe worth a try for you.<br>
<br>
| Simplest case of this is the discretized SDE models, this is the function<br>
| which user modifies:<br>
| <a href="https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp" id="LPlnk406661" previewremoved="true">
https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp</a>,
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<a id="LPImageAnchor_15045495828110.8463423242320118" style="display: table-cell; text-align: center;" href="https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp" target="_blank"><img style="display: inline-block; max-width: 250px; max-height: 250px; height: 250px; width: 250px; border-width: 0px; vertical-align: bottom;" aria-label="Linkin esikatselukuva valittu. Avaa linkki kaksoisnapauttamalla." id="LPThumbnailImageID_15045495828120.5446565755368848" width="250" height="250" src="https://avatars2.githubusercontent.com/u/1560448?v=4&s=400"></a></div>
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<a id="LPUrlAnchor_15045495828140.23892202048038358" style="text-decoration: none;" href="https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp" target="_blank">bssm/sde_functions.cpp at master · helske/bssm · GitHub</a></div>
<div id="LPMetadata_15045495828140.5340400338186864" style="margin: 10px 0px 16px; color: rgb(102, 102, 102); font-weight: 400; font-family: "wf_segoe-ui_normal","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; font-size: 14px; line-height: 14px;">
github.com</div>
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bssm - Bayesian Inference of State Space Models</div>
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<br>
| <<a href="https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp" id="LPlnk150119" previewremoved="true">https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp</a>>
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<a id="LPImageAnchor_15045495830630.032458290440198434" style="display: table-cell; text-align: center;" href="https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp" target="_blank"><img style="display: inline-block; max-width: 250px; max-height: 250px; height: 250px; width: 250px; border-width: 0px; vertical-align: bottom;" aria-label="Linkin esikatselukuva valittu. Avaa linkki kaksoisnapauttamalla." id="LPThumbnailImageID_15045495830630.1889715101010353" width="250" height="250" src="https://avatars2.githubusercontent.com/u/1560448?v=4&s=400"></a></div>
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<a id="LPUrlAnchor_15045495830650.007485300350805635" style="text-decoration: none;" href="https://github.com/helske/bssm/blob/master/vignettes/sde_functions.cpp" target="_blank">bssm/sde_functions.cpp at master · helske/bssm · GitHub</a></div>
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github.com</div>
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bssm - Bayesian Inference of State Space Models</div>
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| and the relevant parts of the package codes are in src/function_pointers.h,<br>
| src/sde_ssm.cpp and src/R_sde.cpp (I don't really expect anyone to read<br>
| through all of these).<br>
<br>
We'd probably need a reproducible example to really help.<br>
<br>
Dirk<br>
<br>
-- <br>
<a href="http://dirk.eddelbuettel.com" id="LPlnk677532" previewremoved="true">http://dirk.eddelbuettel.com</a> | @eddelbuettel | edd@debian.org<br>
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